The Apple guys should have set it up using IMAP if you want to see your mail folders. POP is a legacy mail protocol and does not cater for folders. IMAP, a much newer mail protocol, makes your iPad a 'window' onto your email server.
Do you know how to switch from POP to IMAP? It's usually better to set up a new email account on the iPad using IMAP, wait until you get that working and then delete the old POP account. That way, if you run into any problems, you still have the 'old' working POP account to use.
Tim