[JCBigler]

The Scarlett 18i20 series only has 18 inputs, that's the 18 in the name.

By default, the first 8 are the analog mic/line inputs. The second two are probably the S/PDIF inputs, and 11 through 18 are the optical inputs.

In Protools, they may just show up at inputs 11 through 18.

The routing in the Focusrite control will determine exactly where they show up. When I had my Scarlett 18i20 (which was a first gen unit) I rerouted the inputs so that the optical inputs wee 8 through 16, and the S/PDIF were 17 and 18. There should be a routing menu in the Focusrite Control software that allows you to specify which inputs are going where.

Protools won't usually show the ADAT inputs. It will likely just show the input number or line inputs from the Scarlett, since it doesn't know which inputs are what types, like it does with your Digi 003.

Also, I prefer to clock through Wordclock with the appropriate word clock cable. I've had instances of clicking and popping and dropped samples by clocking through ADAT.