A valid question. This version installs as a totally separate SmartApp, and the associated devices it creates are also completely separate. This is intended as a replacement of the old version.
The old version of the code does still work for the most part. Chamberlain has not actually blocked connections from Smartthings (yet). However, while the old version can still open and close a door, it can no longer update door status by polling the Chamberlain server. For some people, it seems to not really matter, but for others, it's really screwed up routines because the door status is never accurate.
If things seem to be working for you and you'd rather not bother with setting something else up, I'd say keep the old version running. But if you want more reliable and faster status on whether your door is open or closed, this version might be a nice upgrade for you.