highly recommend if you MUST put the 6x9s in the same box that they be in a separate chamber.
tuning subs and coax speakers in the same chamber is a nightmare, and will ALWAYS sound like hell.
id actually just get some of the 5" separates and mount them in the stock rear speaker locations... but thats just my 2 cents.
for amps...
how much do you wanna spend? and how much power do you want?
one amp i highly recommend is the alpine mrp-350, it can be had for $300 canadian... sometimes less if you flirt with your salesgirl enough

i read a bunch of reviews on it, and they all said its way underrated... puts out 400+ watts easily.
i was kinda doubtful, but my friend has a set up for benching amps, so i bought one, and tossed it on.
first blast - 473.32 watts at 14.4 volts at 2 ohms at 0.1% THD.
those are the specs alpine uses to rate the amp, so yes, in my case, and in those reviews i read, the amp is WAY underrated.
i run a single 10" kicker solobaric (400 watts rms max recommended) in a sealed box, and the amp is more than enough to drive it way into distortion.