Internal drives are much faster and more reliable.
External (USB) drives are much slower and less reliable.

So only use external drives for backup (but NOT your only backup, because their inherent unreliability), for transport of data between different machines.

It's useful to store things that you don't mind at all to loose (because they are so easy to replace) also, but I would do that only if space on your internal drives is reaching zero.

Kees