Trouble with 12" Sub and 6*9s in a 6n boot?

[AcidBoI]

Guys, anyone is having distorted or low quality sound output when using 2x 6*9 speakers on a stealth shelf and 12" 1000W Sub?

I was told that air displacement from the sub will effect the 6*9 and can make sound distorted. Anyone had these problems before?

I have 6*9 on a stealth shelf at the back with standard 10cm speakers on the facia. Now I'm going to upgrade with 1800W(not rms) 5 channel amp and 1000W 12" sub, and tweeters at the front which will replace or be added to the 10cm speakers, not sure which is best yet.

What are your views on this?