It is hard to say what you should do. It depends on your email provider and the type of server they use.
But, syncing your email through iTunes is never a good method. You were right to turn it off. Go to your email provider's setup pages and get the info you need to set it up directly on the iPad under Settings > Mail, Contacts, Calendars > Add Account. If they offer it use their IMAP server.
If you have to use POP, you'll want to visit their website email access and delete the emails from your inbox there, or move them to a folder if you need to keep them.
That's all I can suggest without knowing more. Even then, it will depend on your provider. My direct experience is limited to Google, MobileMe/iCloud, and Yahoo.