How do you handle things like Catfolk that appear in both the Advanced Race Guide and a Bestiary book?
That's why I don't plan to keep the content arranged by book long-term.
Multiple things .. races and classes ... have gained additions in multiple books. New Rage Powers for Barbarians, new Bloodlines for Sorcerers, new Rogue Talents, and so on. Organizing these by book would actually be counter-productive for me in the long-run.
For things like classes and races, I "credit" the book in a general list. So I have a "Base Classes" General Article to serve as the Container for all Base Class Articles... and that header lists "from the Core Rulebook: Barbarian, Bard, ..." in a snippet for each book. Base Classes, Prestige Classes, and Alternate Classes each get a "Header" article under the main "Classes" article.
Races get Race Articles. The Monster entry from the Bestiaries gets a separate Monster Article entry. So, Catfolk would have both, with sepearate uses/purposes. Monster Articles are sorted into alphabetical grouping headers ("A", "B", "C", etc.) and have the specific Bestiary in the Suffix. EDIT: There's no reason not to make use of Realm Works' inherent flexibility and redundant options to put them to work representing the same thing in different ways for different uses. This is also something I have done with Locations...a general Location entry for a well-known place, with its common information included -- and a matching Adventure Site Topic with the encounters and such for a specific adventure.
At present, all of this is done in Realms that I have viewed as experimental.. so they are not all consistent. I am hoping to use the Import/Export to move the Mechanics out of them (as one is for Rise of the Runelords, and the other is for Second Darkness) to create a consolidated Pathfinder Rules Realm that I can re-use.
I view the PRD as a great resource, except that it is organized by book, which means you often have to know, or have an idea, of where to start in order to find something. So for me, a single Realm with all of the content mixed is preferable, and treating the PRD as a single source goes a long way toward that.
Having said all of that, what I am doing is for my own use (and any players in my games). I don't have to worry about making something that would confuse others without me being there to explain the rationale, and so on. So as long as I want to put in the effort to do things "my way", I can customize it as I like.. which would not be the case if it was something for sale.