Adding Bungee to Existing Server

So given all the changes with 1.7.9 and bungee lately I'm a bit confused.
Bottom line here is what I wanna do.

Take an existing single 1.7.9 "Online" server and add Bungee to it and link a couple new servers.

So normally id just put the existing server in offline mode and add add bungee.
But with UUID's am I correct in that it will mess up my current UUID's if its in "Offline" mode?

I could be completely wrong, there just has been a lot of new things with 1.7.9, UUID's and Bungee lately and...

Adding Bungee to Existing Server