Comment links in skinned site!

I have a skinned site and keep my blog in a /! folder. I then use PHPinclude to make the /!/index.php appear on my domains index.php. This, however, makes the comments links go to my domains index.php like this: index.php?p=11#comments when i need it to go to /!/index.php?p=11#comments.

Is there something in the controlpanel i can change to make this happen or do you guys know another way for me to include the /! on my index.php without changing the location of /! and getting the comments links right and still keeping the skins functionable?

thanks!