Nothing wrong with Pioneer, but as with anything, you get what you pay for. As far as speakers, they are on the cheaper side of the audio spectrum. Their headunits are pretty great, decently priced, and the more expensive NAV units are superb! To answer your question, you should probably be having a professional install your system if this is fairly new to, but being fair enough, I put it in as basic form as I could below with a crude diagram.
1st- Headunit (H/U) (With a minimium of 2 Pre-Out slots on back, since you are running a sub. One with front, one with sub/rear. If you can can find a 3, you will be able to run a 4 channel amp with the front and rear spots running the cable to the amp.) From headunit, you run your left right coaxial cable to your amp(s) to the corresponding section, i.e. front, rear, sub
2nd- Amp (2 Channel/4 Channel (depending on H/U), Sub) From Amp, you'll run brand new speaker wire, left/right, to the corresponding speakers/sub
H/U
I
I
I
AMP
LR
LR
LR
Speaker
With this setup, you will ignore/avoid factory speaker lines, running brand new lines to each speaker. To get the signal to your amps, you'll be running coaxial cables from you H/U to your Amp. Also, you'll be running separate power wire(s) and ground wire(s) for your amp(s), as well as a remote wire from your H/U to your amp(s). As far as amp tuning, you're on your own on this one, as it's all played by ear, H/U settings, etc.