I'd have to look again, but I think the fuses (or self-resetting breakers) are just inside the drivers door panel, where the other fuses are. I don't remember if there were IN the fuse panel or if they were behind more plastic, but I seem to recall coming across them while I was wireing up the door popper.
Most vehicles have breakers, thermal or otherwise, on the windows. If you hold the switch for too long, they'll pop. They usually reset themselves pretty quickly, though. For a few seconds, there's a bit of a "ohmygod, did I just break it?!" panic...
Is it possible that you just need to lube up the windows? Maybe the motors have too much load on them?