The way to actually tell Gnus where to get new mail from is to set
mail-sources to a list of mail source specifiers
(see Mail Source Specifiers).
If this variable is
nil, the mail back ends will never attempt to
fetch mail by themselves.
If you want to fetch mail both from your local spool as well as a POP mail server, you'd say something like:
(setq mail-sources '((file) (pop :server "pop3.mail.server" :password "secret")))
Or, if you don't want to use any of the keyword defaults:
(setq mail-sources '((file :path "/var/spool/mail/user-name") (pop :server "pop3.mail.server" :user "user-name" :port "pop3" :password "secret")))
When you use a mail back end, Gnus will slurp all your mail from your inbox and plonk it down in your home directory. Gnus doesn't move any mail if you're not using a mail back end—you have to do a lot of magic invocations first. At the time when you have finished drawing the pentagram, lightened the candles, and sacrificed the goat, you really shouldn't be too surprised when Gnus moves your mail.