Is this the new black Mac Pro, or a silver tower? I haven't handled the newer ones more than a quick look but reformatting the new drive (attached as an external) should work, and something you will need to do first. Use Mac OS Extended (Journaled), unless the new model Mac Pro requires something different. I am also assuming this a a HDD as opposed to a SSD, which I also haven't had the pleasure of using (only Fusion drives).
After reformatting the new drive you can use the free SuperDuper! utility to clone your current setup to a bootable copy on the new drive, which is the best way to go, before swapping the drives. If you are dealing with a SSD and this process gives you any trouble, you'll need to install OS X fresh on the new drive and use Migration Assistant to move your User folder stuff over.
Don't stress over experimenting; the new blank drive can be reformatted repeatedly as needed. And don't wipe you old drive until the new one is up and running reliably!