duplicate emails in Mac Mail from Gmail apps account

I just switched my primary email account to google apps. I use mac mail on my imac (and also a macbook) to send/receive emails on that account. Since the switch, I notice that I get a copy of emails both in my top-level "inbox" and also in the gmail "all mail" box (that one is within my gmail section in the left column). I hope I am describing things the right way. I don't want a copy of the mail to go to both places, just to one (my top-level inbox), as it used to. I am using IMAP in my gmail settings. Any idea what is causing this?