First, I'd like clarify that the new Gmail mailbox is not
showing up in two places. The inbox is above and the rest of the folder structure is below.
If you apply some logic to what you're trying to do, it will become clear that it's not very logical
Why? You are trying to put folders that are not part of an inbox
into the inbox: you want to put a folder called drafts - not an inbox - into your inbox. "Drafts" is not an inbox, it's a location. It's a box. It's anything but an inbox.
What Mail does is it takes your Gmail inbox and places it under the inbox section of the app. It then gives you the rest of Gmail's folder structure down below. When you send an email, it will be placed under "Gmail Acct." --> sent mail. When you write an email but don't send it, it will be placed under "Gmail Acct." --> drafts. And so on.
However, as you can see, there already are places in Mail for this - namely, in your first image - under "Gmail Acct."
So to make the aforementioned "sent" and "drafts" messages go into those default Mail folders, along with "Trash," etc, you need to know a few things about Gmail and IMAP, namely that Google's implementation has a few "special" behaviors that need to be configured when you set it up with a mail client like Mail. This is mainly due to the fact that Gmail (online) uses tags and the IMAP standard uses folders - so the tags need to be translated to folders. For more information on how to do this, look here: http://5thirtyone.com/archives/862
So in summary, the way Mail handles these kinds of things is actually a benefit, especially when you start feeding in many addresses at once into the application: it gives you access to an inbox of a mail address and then splits up other structure elements of that address. Of course, Gmail needs to be correctly configured (see the link above).
I hope that made sense!