RRR,
I'm reasonably familiar with how this works, but I can't help you with the details. Speaker box performance is pretty detailed. To get it right, you'd need lots of technical info on the speaker and how it would interact with your box. A rule of thumb, smaller boxes put out less bass which is likely contributing to your issue. I have a similar setup as what you're describing, a pair of 6x9's in a just-big-enough box. They have very little bass response.
I'd give it a go with what was suggested by ch1ll above. If you don't like the sound, you can always just put a cover over the port and you're back to where you started from.
Another thought, can you put the 8" subwoofer in play with your 6x9's? That might help balance out the sound.