Proper channel setup

You can set up your system however you like.  As long as it sounds good to you, that's really all that matter, eh?  But I'll toss out a couple of general comments that you can take for what they're worth.

First, only use "one speaker" for each frequency band in your main stage.  By this I mean use a stereo set or even a custom array, but do not have two drivers in different locations playing the same bands.  In your case, this means use either your door speakers or your kick pod speakers as mains.  Use only one tweeter on each side, properly positioned and attenuated for your main listening positions.

Second, as to rear fill.  This is a completely subjective area.  Many people like running full-range as rear fill, many people use no rear speakers whatsoever.  If you are interested in proper front soundstage, the rear speakers should either be gone or used for ambiance, or positioned so they cannot be heard directly from the front (such as low on the rear doors.)

Third, crossover points.  Running small speakers full-range can lead to at best power loss due to the amplifier being used in low frequency bands where the speaker simply cannot adequately respond, or at worse to speaker damage from bottoming them out.  That being said, it is entirely possible to operate good quality 6" speakers full range and achieve good results.  So for this one I'll default back to point number one: do not use two speakers playing the same frequency band.  If you use a subwoofer low-passed at, say, 100Hz, then all your main speakers need to be high-passed at 100Hz so they do not conflict or cancel each other out.  Some speakers are better at reproducing low frequencies than others.  Some require much higher crossover points.  It depends on the particular drivers used.  5X7" or 61/2" can generally handle down to 100Hz, 5 1/4" may need closer to 200Hz.

Fourth, channel assignment and wiring.  I suggest using the channel assignments of your head unit as designed.  Use the front for front and the rear for rear.  If the HU has a subwoofer output, use that.  If not, use an external crossover with a sub out connected to the rear output for the subs.  As far as speaker wiring, for mains I suggest connecting no more than one speaker or speaker set (woofer/tweeter) to each amplifier channel.  If you use four main speakers, you need a 4-channel amp.  Etc.  I also recommend no less than a 4-ohm load on any main channel, although some newer speakers are being released at 2-ohms mainly to satisfy the younger crowd who have been convinced through marketing that lower ohms = louder, and louder = better.  It's sad.

For subwoofers, use a mono amp designed for subs and if you use multiple drivers, make sure they receive the exact same signal and are properly positioned so they will not cancel each other out.

And lastly, if at all possible only purchase equipment you have actually listened to and decided you like the sound of.  There is nothing worse than ordering a set of $400 speakers off the web because your friend Sammy said they are "da bomb" and then finding out you do not like their sound.  Purchase locally from authorized dealers and only after you have auditioned the gear.  You will be happier and get better service with full warranty, and that is IMO worth it even if it costs you a little more up front.

A 4 channel is not designed to drive subwoofers.  While it will not harm the amp as long as you stay at or above it's rated impedence (and set your gains accordingly), it will not offer the power of a mono amp.  You can use it for now, but you will have more system flexibility when you upgrade- more hookup options, as well as power available.

I agree with DYohn.  Use the front rca outputs for signal to the amp for the fronts, the rears for the rear speakers, and your third set can be used for the subs.

Hi there.  Yes, of course you CAN use any amplifier for any application.  It's just a matter of efficiency and getting the best performance.  A Class A or A/B amplifier can drive subs just fine.  But a Class D subwoofer amplifier will do so at a much higher efficiency rating, using 1/2 or less power and placing far less strain on your vehicle's electrical system.  Plus, the advantage of using a mono amp is never having to worry about imbalances between the two channels of a stereo amp.

For a HU with 4 pre-outs, I highly recommend you use an external electronic crossover that can create a dedicated subwoofer output.  This is far more easily controllable and much more reliable than daisy-chaining amps and relying on the built-in crossovers.