You have to type that as if it was a chat message, then press Enter. Obviously, "password" and "email" are to be replaced with that information. For example:
/msg nickserv register password1234
[email protected]
The password and e-mail can be anything you want, really. You won't need to remember them if you don't usually go to Waffles' IRC (which since this thread exists, is obviously the case).
After you do that, you should be able to /join #waffles.fm-help. Note you must have been connected for a certain amount of time to be able to register your nick, I think it was 2-3 minutes.