head unit vm9311, amp?

Sounds okay to me.

The output from your head units' onboard amplifier will not be affected if you are using RCA cables.

You're question isn't totally clear, but it sounds like you're running 4 speakers off of a two channel amp.  This isn't bad necessarily, but it isn't ideal either.  First, as you already mentioned, you lose fader control.  Even if this doesn't concern you, you still lose sound quality somewhat because, more than likely, your amp will be running at 2 ohms.  Although this will allow for more power, amplifiers have a higher distortion rating when running at 2 versus 4 ohms.  On a sub, that increased distortion would likely be unnoticable, but it probably is noticable on door speakers sinces they're much more detailed than a sub and thus more likely to be negatively impacted by an unclean signal.  Your head unit will still output through the speaker wire on the deck harness, even if you use RCA's