Yeah, you'll want to be using the red connectors if possible to plug in your second GPU. This is because they are all 12V pins, which will share the current load across the three of them.
There's only one 12V conductor on the other modular connections, and that might be a problem if you try and power a whole GPU from one of them, as the cable may exceed it's rated current capacity. If you have to use the 4-pin molex converter thingies, use 1 plug from each separate modular connector breakout. It won't be an issue at all, but lets avoid shoving 12A down one single 18awg conductor of questionable quality in a hot PC case.