It would help if you gave some more details. Are you using POP3 mail or IMAP? Are you trying to add POPFile to a system where Windows Live Mail 2012 has already been configured to handle your mail?

POPFile's online manual has a couple of pages about using Windows Live Mail:

Configure Windows Live Mail for POPFile

Moving Messages in Windows Live Mail

Although those pages refer to an older version of Windows Live Mail, the Microsoft Help pages for the current version suggest that the information in POPFile's online manual is still useful.