Sure you can have both running. Beware funny thing can happen if you access the same mailbox mixed, so e.g. one time with POP3 next time with IMAP, and again with POP3. The 'read' flag on messages may give you some surprises. POP normally downloads mails, IMAP only marks them read. Next time POP3 comes around a 'sees' an already read email. Depends on your client what happens, but I had weird experiences....... Oke, admitted that was like a couple of centuries ago.
As long as User1 uses POP always and User2 IMAP always there should not be a problem. All the howto guides include the installation of both POP and IMAP server.