How to I keep my most used documents open and organized?
If you keep all your commonly used documents open, they should all appear in the Context menu.
You could put them on Favorites and keep the Favorites panel open on the left.
You could put the Note from the Document to the Shortcut Bar. the left one opens a new File any Time if I click on it. The right one opens my Note I'm working on right now.

Why does every Bible or commentary refer me to the Faithlife Study Bible rather than a Bible?
It seems you prioritized the FSB above your bibles.
In the Psalm Explorer tool what is the difference between hymns and praises?
The documentation seems a bit incomplete here.
From the About button one can see the documentation of the data:

which includes a bibliography of where the data is drawn from

Sorry but not having Gunkel I can't provide a complete answer.
http://biblical-studies.ca/pdfs/Gunkel_Classification_of_the_Psalms.pdf provide some of the Gunkel material
How can I avoid scrolling to find the page number?
Click in the box at the top of the panel that shows the current location in the resource. This will open a popup that displays all of the applicable locations at the current position, including page number (if available).

How do I get Logos to select only the word I select, not a phrase or clause?
In program settings set Text Selection to "Word". Yours is probably set to "Smart".
EDIT: You may have to restart the program for the setting to take affect. I'm not sure.

I select and right click; why can't I save as a Clipping anymore?
I suspect that you have the right side of the menu on something other than Selection. Compare below:


Why when I try to priortize KJV1900 do I get KJV with Apocrypha?
Yes, because you are prioritizing a series


Why does copy & paste give me the reference rather than the text?
Here is a link to the wiki page related to screenshots
https://wiki.logos.com/Screenshot
I think what is probably happening is that reference rather than selection is clicked in the menu that comes up when you right click. Follow these steps:
1. Select desired text
2. Right click
3. Left click on the selection option (top right)
4. Click copy
That should now enable you to paste the selection into your word processor
What is a screenshot?
A screenshot is a photograph of your screen... only you don't use a camera, you use software (which may or may not be built into your operating system). See this link: http://www.take-a-screenshot.org
What happens to Notes in Guides?
They are saved in the Guide itself.
When you open a new Guide a line will appear telling you that you have an overlapping Guide saved.

You may also open them from the guides menu.

I use them to contain work notes - how far I've gotten in a section - questions raised that I want to check further on, that sort of stuff. I would use them in a more permanent manner if there was a refresh function that added new sections from the template.
A note on guide notes: Notes attached to guides are saved to that now saved guide rather than all instances of the guide, or even guides that share a similar reference. In MJ's example (Matthew 5:7-8), if she were to add a note to an element like "Commentaries," and then ran another for only Matthew 5:7 or Matthew 5:8 respectively the notes made would not appear in either. Once the guide is modified (in this case annotated) it becomes "separate" in this way. You need to return to that particular instance of that guide to see the notes.
Additionally, if you ever return to this guide by searching for the same reference the saved guide will appear rather than a fresh one. This means if you decide you don't want to see a bunch of commentaries and you delete them, or even a particular element of the guide, the next time you return to that citation in that guide you'll see the guide as you have modified it.
How do I properly read the CNTTS apparatus?
From a blog - is this what you need?
Over the last few years I have been blessed to work with the great scholars associated with Center for New Testament Textual Study (www.nobts.edu/cntts/ and nttext.org/). One of the center’s ongoing project is our New Testament Critical Apparatus. The opening page in the module prepared for the Accordance Bible Soffware gives this introductory information.
THE CENTER FOR NEW TESTAMENT TEXTUAL STUDIES NT CRITICAL APPARATUS
© 2010 by the New Orleans Baptist Theological Seminary
This database is a project of the H. Milton Haggard
Center for New Testament Textual Studies (CNTTS),
a research center under the auspices of
New Orleans Baptist Theological Seminary (NOBTS).
Dr. Bill Warren, Director of the CNTTS
What makes this database truly amazing is the level of information that it provides for the scholarly study of the Greek New Testament. One can get a sense of the tool’s sophistication from the symbols used in communication various information about each manuscript;
OVERVIEW OF CNTTS TEXTUAL DATABASE SYMBOLS
Variation Type (First Column, First Line)
S Significant, this variation unit contains readings that likely are significant for tracing textual affinities
I Insignificant, this variation unit may not be significant for tracing textual affinities except perhaps within smaller groupings of manuscripts
Z Singular, this variation unit only has a single Greek witness to what might be a significant reading or only has Latin support
L Lacunae, this variation unit appears at the beginning of each verse and shows all manuscripts that are partially extant or not extant for this verse or passage
Major Variations (First Column)
A Addition, the reading includes more text than found in the UBS text
M Subtraction, the reading contains less text than found in the UBS text
R Replacement, the reading has a different wording than the UBS text
T Transposition, the reading has a different word order than the UBS text
Variation Code (Second Column)
0 Notation for base text, N-A 27th
1 A reading that represents the base text with only minor differences (orthography, Nomina Sacra, etc.)
2-20 A significant change from the base text with at least two supporting witnesses
50-up A significant change from the base text but with only one supporting Greek witness or a reading with only Latin support
99 Lacunae listed under significant variation units; omitted portions of the text noted in previous units; and instances where Latin witness are indeterminable (e. g. addition omission of a Greek article)
Minor Variations (Third Column)
E Error, the reading seems to be a scribal error that resulted in a nonsense reading
H Homoioteleuton, the reading likely is the result of jumping from like endings
N Movable Nu (+ν,-ν), the reading seems to be due to the movable Nu rule
O Orthography, the reading is likely due to vowel confusion or spelling differences
P Proper Name/Noun, the reading involves the spelling of a proper noun
X Nomina Sacra, a shortened form of a sacred word/title/name has been used
Manuscript Notations
* indicates the reading of the original hand of a manuscript (B*)
c indicates a corrector’s reading in the manuscript (Bc)
mg indicates a reading in the margin of the manuscript (Bmg)
cmg indicates a corrector’s reading found in the margin of the manuscript (Bcmg)
vid indicates an apparent reading (Bvid)
Symbols in Text
lac. lacunae, the manuscript is not extant for this reading or passage
OM Omit, the base reading is omitted
… ellipsis, represents the rest of the text within the verse/passage (μη … δε)
. dots, indicate uncertainty regarding the letters between the dots (.μη.)
[ ] brackets, used to indicate missing text (δε α[υτου])
(1) (2) denotes multiple occurrences of the same word in the verse (και(1) … και (2))
1, 2, 3 the order of the words in a transposition relative to the base text’s order
+ Add the following text (or letter) to the base text
– Delete the following text (or letter) from the base text
sup Supplied, this portion of the text was supplied later by a different scribe
Arrangement of the Readings
The readings for each variation unit are arranged in the following order.
• Orthographic variations
• Additions to the base text
• Omission
• Omissions within the base unit
• Changes within the base unit (replacements, transpositions, etc)
• Singular Greek readings
• Latin readings
• Lacunae
Due to the nature of the readings, some exceptions to the above may be noted.
Have you watched the training video? https://www.youtube.com/watch?v=r7M2C1iBRxE
I've been wanting to redo the whole CNTTS video training, but time has not allowed it. So, instead I redid the video today and simply kept the audio. The new video is better in quality with some callouts and zooming in features. The old video will remain up on youtube, at least for awhile.
I changed the link on the wiki page to the new video.
I also hope to, one day, do a series of videos using the CNTTS not just a video showing how to read it.
Here is the link to the new version of the CNTTS video training.
https://www.youtube.com/watch?v=uI-zxndZQq0
How do I open a collection all at once (not using a layout).?
You can open 10 at a time from your Library. In your Library, to the right of the Find box, click on "All Resources" and select the name of your collection. Then select the first 10 resources, and in the Resource Information box click "Open all". Repeat for the next 10 and the final 5.
You can always open up to 10 resources at a time from the library with one click. Once you exceed 10 the option to "Open all" goes away.
How do I run a concordance search on a Greek word?
Right-click on the word, select the lemma and select "search this resource"

which gives you

My screenshots are from Logos 6 so will show some things you don't see but the principles are the same.