The red one is for the internal circulation fan. FAN1 and FAN2 are actually the same, so you can plug it into either one. There is a great thread on these controllers here:
The tech article really centers around replacing the electrolytic capacitors because they seem to be *very* poor quality. In post #38 there is a link to an excellent thread by another person, but it is all in Spanish:
To cut to the chase, however, the author posts two pages of schematics for the board (mind you, there are a few variations, but the general circuit is pretty similar. There isn’t a whole lot to the concept. The links to the schematics are here:
The red one is for the internal circulation fan. The other two, I believe, are actually the same (for a two heatsink system). But if you only have one fan, I believe it is hooked up to the top (nearest the corner) connector.
Someplace I have a schematic. My external fan died and I wanted to put the schematic with the unit. Now I can’t find the darned thing. If I could, I’d be able to answer you definitively, but I am almost positive that you can put the heatsink fan on either and you’ll be fine.