If you have configured your Mail client as IMAP, you will get everything that is on the server, on your Mac.
Configuring as POP3 should enable you to sort things out a little more easily.
http://mail.google.com/support/bin/answer.py?hl=en&answer=13273 for more info on POP3
I'm trying to set up my Mail with my Gmail account but I have way too many messages on it.
What I would like to do is to sync only what is in my inbox now (I've archived everything older than a month) and I can't seem to get around it. It always ends up trying to sync messages from the "All Mail" folder. I've tried preferences but nothing of the sort.
I'm using a MBP 13" running 10.6.4
Help is appreciated.