I'm using a POP client actually. It can do IMAP supposedly, but I had trouble with it, so I stuck with POP.
As for the mail stuff... that's what I'm seeing. I have a directory called mail, in which is several files containing messages (Drafts, Sent, SPAM, Trash). These seem to be related to the webmail in some way. I also have files named Drafts, Inbox, Sent, SPAM, and Trash in my root directory. The one in the /mail directory was, I believe, created by/with Squirrelmail. The one in the root was, I believe, created by the spam filter code. I'd have to delete them both and see what happens to be sure.
Clearly the webmail app, or my use of it anyway, is causing some of the confusion here.