Yep, I agree with hippy, forget the 6x9's, swap them or sell them and get a sub.
It'll be heaps less work, and sound way better.
If your amp wont fit next to the battery, screw a piece of MDF to the cover that goes across it. Then mount you r amp on it.
Looks pretty neat and is easy to get to. Also allows plenty of ventilation for cooling, (even though you should really mount them horizontally).
A pre fab sub box is not as flash as a full install, but does the job, and can be taken out to make more space.