It's all down to personal taste, some people don't like 6X9's and I must admit all components I have heard sound better than 6X9's. But as for the sub and 6X9's interfering with each other, I run 6X9's and a sub and they don't interfere with each other, my sub sounds the same as without the 6X9's except now I get more than just bass coming from the rear, only noticed if your in the back though lol.
All this said though, I know someone who's got some Infinity 6X9's in his Fiat Punto, and they sound amazing, I thought he had a sub, was well amazed when he said he had one in the boot but hasn't wired it up yet. Problem is he doesn't know what model they are, just that they are 2 years old or so.