Not sure if you still have this problem, but this confused me too.
I have been using Sparrow during Mavericks. After upgrade to Yosemite I decide to give the native mail.app a try.
It looks good, but I was confused that it seem when adding multiple email accounts, it will show the structures, like folders, labels, etc in separate, but has a together inbox, which I dislike.
I believe Apple shouldn't do something this stupid (While sometimes they did...), but anyway I checked everything in the preferences but can't find a clue.
Finally, I found the way they do it....
When you adding multiple account, You still get the separate inbox and sent box and junk boxes for each account.
It is just been grouped together...looking for the small arrow at the left most of Inbox, Drafts, Sent, Junk, Trash and Archive, after expanding them, you will find your account. And you can browser them separately.