system setup

It only has one input and output. I was thinking the same thing, just use a y splitter and run everything through the kicker eq. I also running the remote bass control for the sub amps so that helps if I dont want as much bass, since I would loose the sub control feature off the head unit if I use the kicker eq. Is one way better than the other?

Thanks

Yes, use the Kicker eq as it has far superior capabilities as compared to the basic eq in the Pioneer. If your main amplifier has a set of pass through rca's jacks, this would eliminate the need for rca y cables. If you must use the y cables, consider  an active crossover to separate the two signals after the eq instead. Otherwise the rca y cables are the next best bet.

The downfall of having 2 sub amplifiers is that (unless I am mistaken) you will also need two sub level controls, one for each sub amp. (I read your post as though you had two sub amps, correct me if I am wrong). If tis is the case then I would most definitely look at some kind of active crossover with a included sub level controller. This would solve the control issues that arise with two sub amplfiers and two sub level controllers.