Is there a way to backup and change your blackberry bookmarks on your PC?

Download and install the Blackberry Desktop Manager from your provider (which may link to the Blackberry site). It has a backup utility and bookmarks are backed up.

If you're on a BES with full wireless sync (server 4.x), no need - they're backed up to the server, and restored when you perform an Enterprise Activation.

I was looking more to edit the folders from my PC not having to go thru the backup!

Sorry, there are no tools that will allow you to do this.