The purpose of having both channel inputs on the sub is so that they can be summed to mono. If you are using the two subs adjacent to your left and right main speakers, you could consider left channel to left sub and right channel to right sub. If they are not adjacent to the mains, you should run both channels to the subs and sum to mono.
Regarding blowing fuses, I suspect the fiddly insertion of all those wires into your power amp resulted in a loose strand that was shorting to the adjacent connector. Have a close look. You might be better to make a y connector, assuming you are using standard speaker wire. A short length of wire, then solder the mains and sub leads pos to pos and neg to neg, using shrink wrap or electrical tape to insulate the connections. There is very little current flow into the high level sub inputs, soyou are not overloading the single y connector wire to the amp. Hope this helps.