I just did a system in my car, and found a couple of things. First, fitting modern 6X9's in the factory spot didn't work for me. The new speakers were to deep and the magnets were to big to fit in the original holes. Second, since I carry a few things in my storage compartment and the jack is under it, that wasn't an option for either the amp or the sub, which was an entirely differnet issue, finding a place for it, that had the space the speaker needs. And then the head unit. Like you, I didn't want something that was completely out of place and considered the glove box option, but I use that too.
I went with a Pioneer system. I used the DEH-P410UB head, the TS A4672R 4X6 3 way speakers for the dash, the TS A943P 6X9 4 way's for the back, a Kicker Comp VT8 subwoofer and a Kicker ZX300.1 amp. The amp is only for the subwoofer.
Here's what I ended up with. I keep my iPod in the glove box now too..
It all looks really good. Is your 6x9 boxes enclosed in the back, or is the back the carpet and the 6x9 holes. I still need to build mine, but nor certain if I should enclose all are let the back of the car/carpet be the back??
Thanks,
Hopefully, this gives you some ideas that will help!!