i want to say you probably blew your fuse on your amp and if your not lucky you might of done some damage to your headunit. i would first meter and see if your remote wire is reading 12v with it on and work towards the amp.

Matt86, check the phase of your subs. if one of them are switch than it'll sound pretty bad like that also meter your subs and turn your dvm to check resistance, it should be around 4 give or take an hundredth of an ohm. also could you give a better discription of what going wrong. does the amp turn on, did any of the fuse blow, if so which fuses blew? when did it happen?

i don't think the subs are being underpowered since the subs are 200w rms. i'm not sure what the ratings are for the amp is but should be enough to power the subs. depending on how you wired the subs your running subs 2ohms or 8ohms each in stereo or 1ohm or 4ohm in parallel. i would say running that amp at 2ohms or 1ohms would definately mess up your amp. i'm not sure how well the kenwood amps handles the 2 ohm and 1 ohm load.