In a corrct setup you should do one of the following.
My head unit has rca outs for front, rear and sub. So if yours is the same you should be using the rca's from the sub out to plug into the rear bridged channel on the amp with the cross over set to low pass.
(http://img205.exs.cx/img205/6950/amp17si.jpg)
If you dont have a sub out rca channel on the head unit use the rear outs instead. Then use the front out rcas on the head unit, running another cable to the amp using the front channel with the cross over either set to high pass or no on at all. Idealy i would use the front channel on the amp to power your front speakers not the 6x9's as you will get much better quality of sound with the cross over set to high pass. Just run the 6x9's off the head unit. The 6x9's are really only for people sat in the back. Your sub will do all the bass work and your fronts will provide the quality of voice and highs with no bass. Its all a little confusing so i will draw some diagrams.
Another option if your feeling lazy and a bit cheap is to buy a set of Y splitters for the rca cable. This way you can use the same cable to power both channels on the amp.
(http://img205.exs.cx/img205/6630/amp25ow.jpg)