have you set your gain yet? Also is your amplifiers filters properly set: for example, if it is for subwoofers, you would want the low pass filter set to 80 hz or so, if it is for mids/highs, you would probably want the high pass filter set to about 100 hz...this is depending on personal preference and the speakers though. And if your head unit has a crossover, is that properly set? Or head units Equalizer, best bet would be to make everything flat. Also if you have a dmm, I would check to make sure everything is putting out voltage and such.
oh yea like the last guy said, many head units have a setting that allows you to switch between the rca outputs and the onboard amplifiers outputs, you need to make sure it is going to your rca's. Your head units manual will tell you how to do that. There may also be a Sub-W on setting. Lots of places to check. Back when I was a newb I had that problem once lol. But I didn't have yahoo answers so your lucky in that respect. Good luck.
Also, you should probably join a car audio forum...I recommend
stevemeadedesigns.com
realmofexcursion.com
they have great forums, and those people are WAY more knowledgeable than what you will get on here.