Nice face plate!! that looks awesome! did you buy a replacement and mod it or is that your stock one with modifications?
If i had one that slick - i might change my mind once again.. and put in dash..

(instead of center consol)
My hardware - none as of yet. I have laptops and desktops i am thinking about using - (its a small form factor and need to ensure its atx compliant so i can use a dc to dc PS).
Car stereo questions - thats a no go with subs and 6X8s on same amp.
For a sub - you mentioned 12's - you are going to run seperate power to. Your only going to want to send them low frequencies (most amps nowaday have a low pass filter - which replaces the need for a crossover)
Im still nto sure about the solution for the door speakers.. (the 8's)
Have you taken the door apart as of yet?
To put simply - these stock amps probably have a speaker wire running into them - you could run a feed from a after market amp to this stock ones or just remove the stock amps all together.. (run the speaker wire directly to the 8's from the amp).
OK.. basically what i would try (and im not sure if this would work or best setup but an idea)
You use your 4 channel amp for your 5x7 or 6 x 8s - but here is how i would handle stock 8's I would take the channel you use for your fronts - and basically run 2 sets of speaker wire for each channel. so you would have speaker wire running to your highs and to the stock amp. I think the stock amps have some sort of low pass filter built in. i think this would work and i dont think it will hurt the amp.
This is all best guess - i havent taken anything apart to see how it all works...
some food for thought - how does the stock amps work? (in terms of turn on or remote wire - i am hoping this doesnt come from the stock radio)
anyways.. i hope this somewhat gives you some ideas..