You can't do this directly on the iPad. If you have your inbound mail protocol set to POP you can't do it at all.
If your inbound mail protocol is set to IMAP, then the iPad will reflect the folder structure on your email server. So you'll need to establish the folder structure there that you want to see on the iPad - using webmail - and then, when you open the iPad's Mail app, you'll see the folder structure that you established on the mail server on your iPad.
Tim