I a 600w pioneer 4 channel amp also and im running all 4 of my 5x7 speakers to it and they run incredibly. I dont think you really need to run 2 through the head unit and 2 through the amp. It might also depend on what gauge wire your running to your amp. I have 4 gauge running up to a distribution block which splits into 4 gauge for my sub amp and 8 gauge for the amp( the 8 gauge is only running baout 3 feet though. Also, what gauge wire do you have running from the amp to your speakers? you really need at least 16 gauge (standard speaker wire) Finally check the impedence on your speakers and what your amp is rated at. Dont forget that depending on how they are wired (parallel vs. series) changes the impedence. Here is a sight that might help you decide what wire you need.
Unless your on a budget, runng your subs on a seperate amp will really make a big difference. Hope this helps a little bit since we have the same pioneer amp.