Depending on how you loaded them. If they are carrier themes loaded with the modified BlackBerry.alx file, then follow the following instructions to update your BlackBerry.alx.
http://www.blackberryforums.com/show...&postcount=129
If you downloaded them over-the-air from RIM (such as Smoothie) or from someone on here, then they should appear in Settings > Advanced Options > Applications.
To remove a module that is in use with Javaloader, use the following command:
javaloader -u erase -f <module name>
The -f will flag it to remove an in-use module. If the theme is in-use though, you will likely have a black/white theme once your phone reboots and comes back online.