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A little trick from one imprinter to another, don't ever overlay. Cut them out so one is inside of another if you want the material to last more than a couple weeks. Trust me. You can even call your dealer and they will confirm this as well.
We do 2 color thermoflex plus with some regularity. We usually don't overlay the thermo - we knock out the colors in each layer. Doing it this way I have shirts that have been washed weekly for a year and they are doing fine. When you lay down the first layer heat it only enough for it to release from the liner (about half the normal time) and then do the second color for the full time. We usually lay down the lightest color last if at all possible.
If you try to overlay the second color on top of the first thermo color it doesn't adhere to the fabric like Flame Master said. Haven't tried it but don't think I would recommend doing it that way.