For storing squads, I have to make do with one of those GW cases (received with a stash of Battletech, no way I'd buy one of those new). I still can't work out why they made the rows 9 models long, it's not like anyone uses squads in multiples of 10 models (marines redux?). So I have a sergeant and 8 guardsmen per row, and then I have 1 of the foam trays in the case devoted to all my weapons, HQ, and characters, such as advisors or officers. When I set up my army, it's merely a case of looking at which squads have which weapons, and adding 1 special weapon from the HQ tray to the appropriate squad. Any platoon command members are pulled from the leftover squaddies that get exchanged for heavy weapons, there's usually only two heavy weapons in my 1500 point list, and so it covers the soldiers I need in my platoon command squads.
As for telling them apart on the battlefield, squads are usually spaced apart well enough, and I've familiarised myself with each platoon's weapons loadout. In assault, most units don't last long, and I find that only 1 or 2 squads are needed in all but the largest scraps, and even then, after 20 guardsmenb charge into CC, there's not much room for anyone else to fit. When they die, I allocate a space in the gaming enviroment to each platoon, and they all line up in squads again, ready to be packed away once more. Simple.
