Depends on what ROM you are using. If you are using a stock ROM then they should work just like they did before you rooted. If you are using CTMod, CM7 or 1 of the other ROMs, check the removed app folder in the OP of the ROM. Some of the DEVs remove the live wallpaper apk. You will need to add it back to your ROM if it has been removed.
Try long-pressing your homescreen, then select wallpaper then live-wallpaper.