OP asks:
"Can I use the faster thunderbolt disk as the main disk?"
Yes.
This is your answer.
I suggest you "move everything over" to the thunderbolt drive, and set that to be the boot drive using the "startup disk" preference pane.
If the external SSD is brand-new (nothing on it), the easiest way to do this is by using either CarbonCopyCloner or SuperDuper to "clone" the contents of the internal drive to the external thunderbolt drive.
Both apps are FREE to download and use for 30 days -- this will cost you nothing.
Very VERY easy to do.
Best of luck!