Since the Gmail on your BB is the same as your web-based Gmail, you will need to disconnect your other emails from either your Gmail account or BB...otherwise you will get them twice.
I solved this dilemma of getting things twice this way:
I forward the pop3 to my Gmail, because I like keeping things organized in one place and gmail works for me. When I set up the forward, though, I SKIP THE INBOX on gmail, and send it directly to a folder (or apply a label, in gmail's terminology). So it arrives on my phone from the pop3 account as soon as it comes in; gmail grabs every hour or so and there's a delay, but it eventually ends up in the gmail account, but I don't get a second notification from gmail because it's gone directly into the folder (been labeled) skipping the inbox.
I can show or hide the labels on my gmail, only show them when there's new mail, and it clears the inbox on gmail as well. I can reply with my phone from the pop3 email, or from gmail and my incoming is pre-sorted to labels for me. It works for me - post back if I haven't been clear in how I set this all up!