When i install most new themes, it takes out my adsence and banners rotations, any ideas on how to fix this? Do only certain themes support these mods?
Sometimes you'll need to install mods onto themes manually.
See: Manual Installation of Mods (http://docs.simplemachines.org/index.php?topic=402)
If you're using the ad mod then there are some custom install instructions for different themes at www.smfads.com