I actually do both. Sort by book and have my own custom book source tag entries. which is larger than my monitor can actually show at once.
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I don't know why I want it sorted into books in each of the sections...
I wonder about something... I will test something and be back.
[edit=1] Before the time of computer entitlement, if we sat down for a game of tabletop roleplaying games, we would need all the books to reference and would have to know exactly where to look, that's why book indexes where valuable, bookmarks of varies kinds and paper notes became vital to the game.
Even now, we buy books separated out by content, we buy adventure paths, we download unofficial content via PDF all separated out into subsections, which may or may not at a later date become printed official content. To me, therefore its logical to keep that formation when imputing content. Errata's come out with book and version numbers. We get the information from a book it would seem logical to keep that in book form for data entry.
Even D&D Beyond separates its books out, heck it separates it out per chapter.
My long term goal is to have each book in realm works as its own separate realm, and when I need to, import the contents into the realms that needs them. [/edit]