That's exactly right - you probably need a spacer. I currently have 6x9 Infinity Kappas' in my doors, but these came with a separate 1/2" spacer.
I had a different pair of 6x9s that had a spacer glued to the front of the speaker. It wasn't too hard to remove the spacer from the front to use on the backside - just be careful to not remove the cone surround at the same time!
If you'd rather not go through all the trouble, then get the Pioneer 6x8 3-ways. Not as much bass as 6x9s', but very clean sounding. I've had 5x7, 6x8 and now 6x9 installed in my car. It is definitely worth the trouble to install the bigger speakers.
-Wes
98 SE Sport
