Mod Rewrite problems (problems caused by Mod Rewrites?)

It would be handy to know your actual site URL and wheather you are using a content management system.
also are you running your own server and is it IIS or Apache (or something else) ( I assume apache as Mod_rewrite for IIS is very hard to do)
If you do implement a mod_rewrite your team may have to rewrite the links manually or else use a redirect which will mean serving 2 pages for every link clicked.
if you are using a redirect make sure its a 30q redirect in order to make it search engine friendly.
Also stuff like image code may have to be rewritten or you may have to create dupicate directories for the same images.

EG: yoursite.com/site?section=category has an image located in yoursite.com/image.jpg with mod_rewrite enabled the page code looks for the image at yoursite.com/catagory/image.jpg

you should be able to create automatic rules in Mod_rewrite that take care of everything, but its not easy.
it would be better to see your URL and your mod_rewrite httaccess code.