I tried Inbox for a few weeks but then reverted back to Gmail. I used labels quite well too. I loved Inbox classifying my mail, it was a breeze to find emails from trips etc, removing clutter, I liked the remind me later feature too.

After a few weeks of usage one thing that bothered me was that Inbox was slower. I continued to use it until I found that I had missed a few mails because Inbox had classified them incorrectly. I figured I'd rather use Gmail and make sure I didn't miss any mail, even if I have to sift through a few more mails. It basically comes down to what you prefer to tolerate type 1 or type 2 errors. And, search has always been good.

In my experience inbox does not modify the way anything is stored, just alter the representation. The same labels as gmail are used so you should just be able to switch back and forth.

What happens in Gmail when I mark something as done in Inbox though? FME, it gets archived, which I really don't want.

The inbox label gets removed (which is called done in inbox and archive in gmail)

I doesnt screw them up, and the Inbox UI has a "gmail" link that gets you gmail view of the same inbox for when you want to do something the Inbox UI makes difficult.