If your email account is an IMAP account, you can create new mailboxes in order to save emails.
If you go to your email account in the Mail app and look at the window where your inbox, trash folder and sent folder are - if there is an Edit button at the top of the window - tap that and then tap Add Mailbox at the bottom.
If the Edit button is not there - you cannot create folders on the iPad. Your email account is not IMAP. Only IMAP email accounts can create folders on the iPad. Any folders that you would already have in an IMAP account would sync to the device as well.