How do I find all references to the 'Spirit' in the NT and how He is referred to?
Try using Factbook and the "Referred to as" section

Bible Search Analysis could also be helpful:

How would I search for a topic or word that is in proximity to a date range?
The date datatype is pretty flexible in its syntax.
For example, you can search for: <Date 1st century AD> to find any dates in the first century.
Or search for: <Date = 1st century AD> to find references to exactly the first century.
Also valid is: <Date late 1st century AD>
Or: <Date mid 1st century AD>
You can also right click on a date and select the date on the right side of the context menu, then select the "Search all resources" option to find the valid way to refer to a particular date you might find.
If there isn't a flag icon (and the "Timeline events" visual filter is turned on), then the date has not been tagged, and you won't be able to search using the Date datatype as shown above. The date will also not show up in the right click menu.
You can look through the Timeline tool for other possible uses. The date rendering on the items in there are all direct renderings of Date references. The only other particularly useful feature I spotted there (with a quick scan) was the ability to specify ranges as part of the reference, millennium references, and use of "ca":
<Date ca 2400 BC - mid 1st ML BC>
How do I make the ESV not LEB show up in reference links?
You need to prioritize the ESV as your highest bible - either in the Library (select ESV and prioritize it to the top) or from the Home Page (choose preferred bible).
How do I tell what page I am on?
If it has page numbers you can do a couple of things:
Click on the location information and page number will be displayed

or enable the "Show page numbers" visual filter

How can I remove the yellow highlighting?
The yellow highlights are temporary, and all related to your search. Close your search window, and they disappear.
How can I get Logos to open where I left off?
Go to Tools, Progam Settings. At the top you will see "At Startup Open to…". You should change this to "Most recent layout (Any)" or "Most recent layout (local)".
How do I read two books in parallel?
If I am understanding your question correctly, I know of two ways to do this.
1) If you have "Logos Now", you will want to use the "Multiple Resources" button.

2) If you don't have Logos Now, you can open two Bible versions side-by-side and use a "Link Set".

How do I use a Logos Mobile-Ed course?
The Mobile.Ed courses are videos, a textbook with transcript accompanying the videos, and an audio version of the videos. So you get - according to the product page - six hours of video training by Professor Darrell Bock, a world renowned scholar. The textbook would probably be several hundred pages if printed as a book.
Included into the courses are some Logos usage training sections, unit quizzes (multiple choice) and two exams.
Regarding the "suggested reading" and "see also" books, the courses I've seen so far don't interact with these, so there is no strong emphasis on selling those. Each course has a Faithlife group which shares a note file for these additional readings and a spreadsheet giving the names of those resources and how often each are referenced. Often, they give three or four suggestions that treat the same material, but one wouldn't need to have all of them.
Typically, the courses assume a platinum level library which should give access to most of these readings. I'm not a platinum owner but buy widely beyond the packages, thus I fare pretty well.

Mobile.Ed are much better than the classroom video captures found on Youtube or iTunesU - I personally compare them to high-quality Udemy courses (such as those taught by NT Wright) and find Mobile.Ed better in terms of the full transcript textbook and the complete integration into Logos. The filming by Logos is much more professional (actually too sterile for my liking, but that's taste, not content), too.