That's a great question, Hopefully this is some what helpful.
#1.Pick a location and know what kind of fish happen to be there and what spots i'll be fishing from.
#2.Pick a fish i'd like to target, It could be bass,rainbow trouts, panfish, all of them.
#3.I will then pick and choose lures to bring with me based on what has worked, location and fish and water depth.
I really wouldn't want to bring a crank bait that is big and can go a depth of 20-30 feet and use it in shallow water.
However, I will still pack and bring lures i have never used before or caught anything on but only a few of them.
#4.After all that, I then pack the lures accordingly.
Each lure gets packed into their own small zip lock bag.
After that is all done, all of them get put into their own category bag=Crankbaits,Frogs,Spinners,Power bait,etc.
In this case, they are packed into one gallon zip lock bags.
Plastics get this treatment, Kept in their original bags and put into a large one gallon zip lock bag.
If any plastics are not in a bag when i get them i put those into small zip lock bags and put those into the large zip lock bag.
#5. I put all the one gallon bags into my backpack and i'm off the fish!
When i get home, I will take the lures out of the bags and hang them up to dry and air out.
Not plastics though.
Edit: My tools go in the very front of my backpack for easy access.
I do have a pet but she is not tall enough or big enough to get her mouth on those and most times my door is shut so she's alright