there is a reason why it has 2 4 guage inputs, to use them both. if you didnt need both, it wouldnt have em.
spkerman is correct about it being paralleled inside the amp, just like the 2 sets of speaker connections that idiots claim it to be a stereo amp, lol. but you have to truly ask yourself do you feel safe only using one set of connectors? starving an amp can make it fail.
running 4 guage back to a distrobution block and then splitting it with 2 4guage wires doesnt give you any more current than one 4 guage can handle. feel free to kick yourself in the azz for that one. i also suggest you pull your head outta your azz when installing. a 100 amp fuse for an amp that will pull around 290 amps at full tilt, wtf made you think that would be sufficient? Not trying to be a dick man, but heck, your on your way to frying your ish. think of your power wire as a fuel line for your top fuel dragster. you gonna run fuel line to your dragster the size of a toothpick? no, you would starve your dragster.
also, i prefer to keep a battery by the 2500d instead of a cap.
one thing you havent said is how you have your amp set up. take a look at this pic and tell me where you are according to it
also, do you have a digital multimeter? please check the ohm load with the dmm. are the subs dual voice coils? are you hooked up to both?
what deck are you using? what voltage preout does it have?
prefab boxes are not usually built for the woofer, mainly built for generalization. I have seen some that hammer in prefabs, and seen some that make you wonder wtf!?!?! .
troubleshooting another 2500d the other day, the guy was noticing he wasnt getting any output on his 2500d like what you are saying. he checked my pic, answered my questions, and then tried one thing for me, which was to click that master/gain/copy switches back and forth a couple times since sometimes dust can get in there and stop it from making a good contact. fixed his problem.