Take a look at your email settings in your Settings app. I, too, have to deal with a POP account and two iDevices. I usually read my mail on the iPad, but sometimes, I still want to look at it when I'm out and about with the iPhone.
In my POP mail settings, I set it up on the iPad (under advanced) to "Delete from server: When removed from inbox." On the iPhone, I have it to never delete from the server (cause my main management is on the iPad, the phone is for just in case viewing). So, if I read the e-mail on the iPad and then delete it - and do a refresh/fetch mail - I find that that particular mail won't download to my phone later. It's not perfect, because sometimes the sync isn't immediate, but it does help to keep down the repeat e-mail downloads.
Maybe this process will work for you? If it makes sense, give it a try, else, let me know and I'll try to clarify my process better.
Good luck.
Marilyn
P.S. Your best bet is to try to see if your provider has an IMAP service. Mine doesn't (TWC Roadrunner), so that's why I had to develope this convoluted process with a POP account....