If you were able to go into recovery and do a nandroid backup, then clockwork is already installed. I would recommend not using Rom Manager as it is buggy. I prefer doing everything manually. It is a good idea to get comfortable with the manual steps as you may need it if you ever get stuck in a boot loop or stuck on the splash screen after flashing. TB is good for transferring your apps when you switch roms, I would be careful restoring data though as it can cause conflicts that make diagnosing difficult at times.
As far as flashing, if you are flashing a rom, then do a full wipe(I use Caulkin's Format All). If you are flashing a kernel or theme then only wipe Davlik-cache.
When you get ready to flash a rom, there is some info you need to verify to make sure your radios are current for the rom you will be flashing. We can cover that when you are ready to start your new addiction