I never did figure that out, nor put much effort into doing so. It probably has its own little config file that's not easily accessable, but it might use registry entries.
If you need to export them, though, you can just click Bookmarks > Manage Bookmarks and go to File > Export Bookmarks in the managment page. I've done it a dozen times with mine. You have to manually move the toolbar bookmarks into the toolbar folder, but it works perfectly aside from that.