To do this you need to do two things, because the native iPad Mail app cannot create mail folders.
First you need to switch from the legacy POP mail protocol to the more modern IMAP ... You can do this in 'Settings', 'Mail, Contacts, Calendar', 'Accounts' and then edit the account to use IMAP.
Then create the folders you want to see on your iPad on your mail server using webmail. Now, when you start up the iPad's Mail app you'll see those folders on your iPad too.
Tim