Keeping emails on the server when using an iPad 2 for email
The iPad supports 2 Mail mechanisms that allow you to do this, IMAP and Exchange.

Both of these mechanisms allow the server to control the status of mail messages, whether they are read/unread etc, what folders they have been moved into.  If you use either of these mechanisms then you can expect to see basically the same content no matter what you use to view the mail on.

The key is what email service you use, as to whether it supports IMAP or Exchange, or something older like POP3 that will now allow such consistent mail states.

iCloud accounts from Apple effectively use IMAP behind the scenes.  GMail can be configured to use pretty much any mechanism, and so can also be happily used.