Definitely not an expert but a lot of experience in car audio.
I would go with what you are planning. Turn the 6x9s down enough you just can't hear them from the drivers seat or you will get a horrible delay (echo).
For deck I would go with kenwood or pioneer.
Amps rockford fosgate or jl.
Speakers rockford or jl. And a good quality 10" sub.
You will probably need to run 2 4 channels amps. I would do a 4 channel for the (4) 6.5s. Then run one set of rca outs to the front 2 channels of the second amp and bridge the rear 2 channels for your sub.
The other option is to run a 5 channel and then run the rear set of 6.5's off of the radio.
There are a lot of other good quality amps/speaker brands out there but they are not as well known. But this all depends on where you want to buy stuff and what you want to spend. A few great company's I have used are:
http://store.crescendoaudio.com/
http://www.sundownaudio.com/
http://hybrid-audio.com/