Cannot get apple mail and gmail to sync properly

I use apple mail for my gmail account. the messages dont seem to sync properly - eg i try to empty the trash and they pop back in there. i changed the settings to what google say to use but now it is downloading 13000 messages. I loged onto my online account to try and delete them from there but i cant find them
What can i do?

Not exactly sure why you cannot find them on the gmail server when logged directly into gmail unless it is due to the fact you set up the gmail preferences to make gmail act as a mail server which I think you have to do to use a mail client.
At any rate, check Mail.app's preferences, accounts, click the account in question, then the Advanced tab.  If you check the checkbox "Remove copy from server after retrieving a message" then the mail won't be saved on gmail's pop server.

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