Notes may seem straightforward but when I started about 5 years ago I experimented with a few different ways of keeping notes.
I have the book Bible Readings for the Home. In it, all the Subjects are covered by topic so that most of the Bible verses are grouped together by Topic. This is the most convenient way to gather information and find it later.
I first tried to use one big note file in the Documents menu under "Notes". I think I named it KJV Notes or something like that. I found that is the way most people do it, but It was too hard to keep things straight so that I could find things later. I was underlining and highlighting and adding Icons to subjects etc... I soon found out that it was better to have many different note files.

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How do you do that? First I got advice to do it by Bible Verse or passage. That is OK if you are making commentaries on each verse as you go while studying, but that didn't help much when trying to recall by Topics such as faith or Grace. "Where did I put that comment?"
The best method I found was to name every Note document by first the type, then Subject. Example:
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As you can see in the screenshot above there are two "Types" (Symbol and Topic) of notes. At the top they start with Symbol type, then after that, the notes are Topic type. That way all theTypes are first sorted alphabetically then topics notes are alphabetically sorted according to the subject. The first note that I have in the Topic type is Topic - 3 Angels messages, The. I store all my Bible verses and book quotes on the subject in that note file.
So far I have just a few Types which I can use to sort the notes Below is listed the Types that I use and their use:
- Bible - ??? This is for Bible Subjects like People in the Bible and who they are, or places in the Bible and where or what they are. Also for specific notes about the Bible or that version of the Bible, or notes that span the whole bible. Examples are Bible - Pople, or Bible - Places, and Bible - ESV, etc... I have abandoned this for new Types called People - ??? and Places - ???
- Book - ??? This type is for making notes on non-Bible and other books in the library. When reading books you can highlight and mark and take notes on these books. That way all your notes on that book will be in one place and make bookmarks for you and notes. You can also make the subject the author so that all notes by a specific author will be in one file. The books will be sorted in the file alphabetically Example: Book - Josephus, Works of. I have kept quotations and notes on the things that Josephus said concerning Jesus and the Bible in this file.
- Definitions - ??? This type is for defining words in the Bible or other interesting facts. Example: Definitions - Bible KJV, and Definitions - ESV
- Outline - ??? This type is for taking notes on Bible passages and verses in the Bible. A commentary type of note. That way you can look for notes about Jeremiah in the Note file; Outline - Jeremiah, then look for the chapter and verse inside that file for notes about that verse specifically. Example: Outline - Jeremiah, Outline - Revelation, Outline - Daniel, Outline - Genesis etc... Inside I make a new note for each chapter and then in the notes area I can write the verse and then the comment. That makes it easy to find any comment that you have made on that verse. You can link any other note or book location to it also with the link Icon at the top on the notebook menu.
- Parable - ??? This file is for notes on the different parables. Example: Parable - 10 Virgins
- Person - ??? This file is for collecting information on certain people of the Bible. It is duplicate of the file in the type Bible - People. I recently don't use the file Bible - People anymore I have separated each person to a unique file. Example: Person - Rahab, Person - Esau, Person - Elijah or Elias, etc ...
- Sermon - ??? This type is for collecting information for sermons. Example: Sermon - How shall we Worship God?, Sermon - 3 Angels Messages, etc ...
- Symbol - ??? This type is for defining symbolic words in the Bible and the verses that are used to define them. Example: Symbol - Bread, Symbol - Marriage, Symbol - Woman, etc ...
- Topic - ??? This is the largest type that I have because this is my favorite way to store information. Topically. Kind of like Nave's Topical index. or Bible Readings for the Home.
Here is a screenshot on how the Outline type is done:
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You can see that Outline - Jeremiah is opened to Jeremiah 2, and Jeremiah 2 is linked and opened from the link in the note file by clicking on the text on the note line. Also if the note is displayed in the Compact form it will open to see the notes that are in that chapter. When I put a Bible verse in the note it automatically makes a link to the Bible verse so you can jump to it. You can add cross-references here or other notes. You can see that hovering over any of the Bible references will open a popup window to display that verse (Jeremiah 2:4).
You may want to use another name for this type. I started out using this type to store outlines of each book from the Bible Commentary so that I could have an overview of each Book of the Bible, but then I expanded it to make commentaries on the book of the Bible. The point is to organize everything so that it is accessible and easy to find for you.
As for the quantity of notes. You can store as many notes as you want. It is stored in the Logos cloud server and locally on your computer. It is all text files so the data size is small. They do not have a limit on the quantity or size of notes you store. Most people don't store many at all so make up for what they don't store.
I hope this helps? If anyone else has a different strategy for notes please share it with us to help with better ideas.