Gmail not deleting the emails? Should I use IMAP or POP?

I have Gmail for my 3rd party mail. I am using a 8310 and I am using BES and BIS, BES for my work and BIS for my gmail. I originally used POP3 for my gmail account and it didn't reconcile what I read or deleted. I read about IMAP and I just tried syncing that up with my gmail account and it still doesn't seem to be reconciling the messages correctly. Any clues as to why this is happening?

because BIS doesn't always reconcile. some do and some don't