With UOAssist, all I currently use is Organize agent to move all my fish, crustaceans, and rewards into one pack. You only have to do 1 agent for the different body types, (both grouper-style fish facings, both dorado-style (catfish, amberjack, etc.) fish facings, both pike-style facings, both trout-style facings, and the 4 original fish body types), that works for all three fish categories (Shallow, deep, dungeon), and of course, adding the 2 crab facings and 2 lobster facings, 1 bait cup of any bait, and 1 hook). This leaves small fish in your main pack, as well as books and PS.
It would be possible to set up another organizer bag with the 8 footwear and the small fish, then toss the bag (and change the target bag) as needed, but I just drop them to decay, or merge them with BODs as needed, and consume all the magical fish (the truly rare fish are good for recalling heavy out of a dungeon, as the three magical fish that buff go off as their equivalent low-level mage buffs cast at GM Eval (Strength, Agility, Cunning)).
I keep my Giant Beetle with me when fishing, as all unneeded fish get taken to my alliance's communal fish boxes. When I hit weight, I open the bag I sorted into, and my beetle. If I'm on my ship, I'll take each fish stack out, and if it goes into one of my quests, I drop it into the matching quest crate (part of it if there's more than the quest has left). Fish not needed get sorted neatly into the beetle for transferal to the communal boxes. After all the fish types are in the beetle, then you can just drop them onto the beetle and the stacks stay neat.
In the storage house, it's 1 box per "Book", with 1 pack per body type in each box (treating the original 4 as 1 type), with the boxes engraved as to which book they correspond to. The Crab/lobster box is slightly different in that we put all the plain ones in one pack, the named crabs in the second, and the named lobsters in the third.