Once we got over 200 quality charts, I found that the boxes are the only way to go. Normally, we leave them at our rehearsal location (which has secured storage), but for a job we have gotten into the habit of pulling all of the charts ourselves, and then storing them in set folders in the front of the boxes.
Occasionally, when presented with a performance site that involves too much rough terrain cartage, we will pull all of the charts, place them in the set folders, and then place all of the set folders in one box and just cart that to the performance.
Usually, though, we just haul all of the boxes - that way I can sub in requests as required. The boxes fit neatly beneath our EmBee fronts.
As for hauling the boxes, all of our "small items" are contained in the selfsame filing tubs. Hat mutes and mute stands in one, sound snake in another, cables in a fourth, light snakes in two more, lights in one more, and so on. They all stack up nicely in the trailer, with the piano and baritone placed on top, and with trailer bars to hold them all in place.
After much trial and error in the early days, I worked out a "load out/load in" protocol that eases moving into a venue for the set up before a job, and for the tear down afterwards. There is even a space marked out on the plot plan where we "land" all of the stuff when moving it in, and then move it manually from there as it comes up in the set up process. (This was added when we found that catering folks were occupying all of the open space in front of the stage. Normally, it's in the part of the dance floor up against our setup site.) Normally, my wife and I do most of the set up (thus ensuring that it gets done right), but we also get help from the drummer and guitar player on most jobs, and tear-down help from everyone before we pay at the end of a job.
For the haulage, we use the smallest size of the Rock 'n' Roller cart. They fold up super small, and are suitable for most hard surfaces, carrying hundreds of pounds if needed.
The two small Rock 'n' Roller carts get tossed on top of all of that other stuff in the trailer. The file boxes stack neatly on the carts, and depending upon the surface on which they are rolled, can carry up to twelve boxes per load. Total move in/move out comes to something like five cart trips plus three "manual" trips (carrying stand bags and rolling other items with their own rollers, like the mike stand bag).
Microphones and sub mixer are in Pelican cases that also get tossed on top, along with the catch all "gig bag" duffle bag (tools, parts, spare pantihose, gaffer tape, CDs and business cards and all sechlike), and the speakers, mike stand bag, monitors and mixer all fit behind the boxes, with the stands and my small horns in the Scion xB that is our new "prime mover".
At our Reliant Stadium convention center job last summer, each cart load had to travel about an eighth of a mile from the trailer to the off-loading point. Even with all of the grief that that entailed, it still went smoothly due to advanced planning.
As I have said on many occasions, the time I spend playing music is miniscule compared to all of the administrative time that I spend. It's in many ways similar to what the Navy and Marine Corps do when putting together an amphibious landing, only without the boats. And, it's a lot of work to do it all right. That's why I get paid those extra bucks...