I have a big 'ol kid's school/duffel bag from Wal Mart. Sits flat, on a rubberized bottom. Has nice zippered side pockets that fit plano boxes perfectly, mesh outer pockets for scissors, tools and other misc. stuff, and a big, open middle section. It looks just like the expensive tackle bags, but only cost something like $19.
As far as where I keep my stuff...
Soft plastics- I keep in separate Ziplock bags in the middle.
Jigs, scissors and superglue- I keep in a big-mouth clear screw lid canister that caramel popcorn came in.
Small jigs, hooks, crappie-lures and so on go in a plano box
Everything else goes in a different plano box or in a ziplock bag, depending.
I carry a LOT of stuff, so my bag weighs as much as a TM battery! The demise is always the handles tearing out. When on the boat, I put it in a corner that's out of the way, and unzip it enough to get in, and I can get to everything in a seconds.
This system works so well that my lazy friends are in the bad habit of just getting stuff from my bag, because it's easier than their complicated "tackle" systems. When I tell them to get their own stuff, they whine like a 3 year old. Losers!
-TH