A question about syncing the IPad with Win XP and Win 8.1
Are you using POP3 or IMAP for your email?

If your service is POP3, then each machine will download emails unread by that machine, up to the retention limit of the mail server.
This means that you will always have to manually delete each email from each machine. 

There is the possibility that you can adjust the retention limit, to reduce the amount of backlog that is downloaded. The retention period usually starts after the first device has downloaded that particular message, so you don't lose any mail if no machine picks up messages for a few days etc. You would need to ask your Service Provider how to do that.

If you use IMAP, then the emails actually always live on the remote server, so any action you take will be reflected across any machine that accesses that remote data.

Which of those services you use is usually not choosable by the user, it's in the hands of your Service Provider.