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One of my friends with an IG army painted his guys with different colored helmets so he could tell the difference. Most were neutral colors so they didn't screw up his paint scheme but made it very easy to tell what guy belonged to which squad. Painting bases (or just the outer rims of them) is another way to work it out.

If you are going to be swapping heavy and special weapons around all over the place, you could make something interchangable on the bases. For example lets say you have 3 squads whos' bases are red, yellow, and blue. You could then have your special and heavy weapons guys modeled up so that there is a magnet on their base (under the base or modeled into the top...whatever works for you). Then you could have little strips of cut sheet metal (or other magnets if it doesn't end up being too strong) in red, yellow, and blue. Now all you have to do is put the colored strip of your choice on the model you want to be attached to each squad. Its a little extra work on the modeling end, but its fairly simple and means that you don't need to have a bunch of extra guys sitting around in your case.