Ok, in general I store them by type of bod. Its cute that bod books can sort by Tailor/Smith/Inscription etc. but I would never mix them in books because I'm working/filling one type at a time. Having more than one kind in a book only happens for me when I make a mistake.
Within the types of bods it depends on how big your collection is. At small collections (5k or less) then I would say sort them by large bod type:
Tailor
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Tailor Large Bod Book
Cloth Smalls
Bone Smalls
Studded Armor Smalls
Female 6 Piece Smalls
Male 6 Piece Smalls
Footwear
For Smith
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Smith Large Bods
Iron Smalls
Iron POF Non Combine (shields and such that don't combine into a weapon or armor large can be upgraded to DC and beyond for Powder of Fort)
Ring Mail Smalls
Chain Mail Smalls
Plate Mail Smalls
For Alchemy (only explo and poison larges really have a good reward with the dye)
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Alchemy Large Bods
Alchemy MIsc Bods
Alchemy Explosion Smalls
Alchemy Poison Smalls
As your collection grows you can expand the number of sorting of books. If EA would have ever added a 'alphabetical' sort to the bod books you wouldn't have to do this but I sort mine by name at some point.
Example :
Footwear (Tailor)
------------------------
Sandals bk1
Sandals bk2
Sandals bk3
Thigh Boots bk1
Thigh Boots Bk2 etc
I keep them to either 100 or 125 in a book so that its easy to put in your back and remove stuff when you have a full pack. As I fill up one book with 125 - I start a new one. The highest number is always a partial book.
When I collect bods I have a 'Tailor Unsorted' and 'Smith Unsorted' in my back and I fill them up. Once they get to 100 or 150 or so I sit down and sort them into their individual books on my vendors. I hold my books on vendors because it would be storage prohibitive to do so in a house.
I've asked several times for them to make bod books like SOA, PS and other books - 1 lockdown per book. Then I wouldnt' need all these vendors cluttering up people's screens when they walk by my house.
Edit: I also didn't explain why I have them sorted like this. The idea of bod sorting is for filling them and usually fitting into larges. The larges are your best bet for points and rewards. Not many small bods have a worthwhile turn in point except for smith smalls that can get you powder for fortification (DC EX 20 and up or gold 20 normal and up). With bribing you can bribe things up to get a better bod so having the same kind in a book makes sense.
For example if I'm filling a Barb kit worthy 20 Female Horned Ex 15 set here is how I work. If I am looking for a Female Bustier 15 Horned EX bod - its best to look in a book of all Female Bustier bods. Why? Because if I don't have the 15 Horn ex - my next best option to bribe up is a 15 EX spined because there is maybe a 70% chance it will go to Horn 15 ex and 30% chance it goes to spined 20 ex. If the later then I put it back in the book and bribe another 15 spined and resort to 15 leather ex next. Or 10 Horn ex etc. At any rate, if I have my female 6 piece smalls across 4 or 5 books and all 6 kinds mixed - I have to go to each book to look for horned 15 ex bustier that might or might not exist. Having in 1 or 2 books right away allows me to grab it or grab a bribing bod or two and head to the tailor to bribe up. I fill by larges I get as I always have less larges than I have smalls to fill. So the smalls set around till I get a large then I bribe ones to match if needed to fill it. I may start by bribing the large to a reward I like. Depends on the cost and how far the large needs to be bribed. Bone larges I likely won't bribe all the way to 20 Barb ex for the barb kit - i'll just go high enough for a horn kit - whatever bribe chain that is - then don't waste any more $$ bribing and try to fill. Always try to keep your bribed larges to lowest leather and quantity if possible.
Just in case people don't know bribing goes as follows :
When you bribe - it can increase the Quality (normal to ex), quantity (10 to 15 to 20) or the material (Leather to Spined to Horn to Barb).
If one of those options is not possible -then it will default to one of the other two (example : cloth can't be anything but cloth so it will only upgrade quantity or normal/ex).
I have no proof but in general it seems to upgrade Material most likely, then quantity, the quality. IE - if you bribe a leather 10 normal bod here is the most likely outcomes :
Spined 10 normal
Leather 15 normal
Leather 10 Exceptional
For this reason is always good to start with the quality level you want then muck around with quantity and material. You are less likely to see a normal bod upgrade to ex if all 3 options are in play. Now with cloth - if its already 20 nm cloth - the only option is 20 ex cloth so it will upgrade.
Hope this helps. I could write a book on bods but then like 4 people would read it. I have 30,000+ that I can never really get on top of.