gmail IMAP Labels Issue

So I'm pretty excited I now have IMAP enabled for my gmail account. However, I don't like the way Mail (or maybe it's gmail) handles sorting my email messages. The gmail labels at the bottom of the left hand panel of Mail show whenever I get a new message AND this message also shows up in my inbox for whatever email account it is in. So if I get two new email messages the badge icon in the dock shows four new messages, which I have to click on in both locations (Inbox and in the corresponding Label folder) to mark as read. I would prefer to use Mail to sort all of various email accounts into folders I set up under "On My Mac" rather than use the labels from gmail. I can't seem to remove the gmail accounts from showing up in the left hand panel of Mail, which would be ideal.