If you are getting fronts and subs you really won't need them, and I'm sure your system's sound quality will be better with them unplugged.
Because they play higher frequencies as well as lower frequencies, they will pull the soundstage (where you perceive the music is coming from) towards the back of the car when it should be focused in the front where you are.
The fronts will play the mids and highs, the subs will play the lows and if set to the correct crossover frequency, shouldn't be directional. So you'll hear everything you need without 6x9's.
Fair enough though as you've already bought them. Try them in for a week and out for a week, setting up your system to sound best to you each time, and then decide.
Oh and when you get the amp, simply run the 6x9's off the HU. You'll only need to amp up the fronts and subs. Those two are the most important to be amped for sound quality.
