Really... I find there are two choices! 1) Leave all the extra clutter at home! Or 2) Get things really organized at home to be able to quickly set milk crates and coolers right into the boat and go!
I got away from Milk crates and went to the good old Playmate Coolers! A larger one with ice as a fishwell and then two smaller ones, different colors to hold different stuff... each is a simple tether within the boat for "flipping"... Flip tops are quick and easy and stay put with rubber matting on bottoms to prevent skidding around and cut noise.
Snag things a lot less with fly fishing and all!
Carry two smaller ones and rod to truck... come back with trailer when I'm done, so rod not left on dock...LOL