FRIGI-BEAM: Sentinel Mark V can use Incapacitate. When it does and hits, choose one: a hit character can't be moved by any game effect until your next turn; or a hit character receives two action tokens.

My question is does the Sentinel use incapacitate normally IE adding a token and then in addition to that it does the "choose one" part or does it do the "choose one" instead of the incapacitate power?

You hit first then choose. You miss, you don't choose.

So, yes, you use Incap normally then you choose the special effect.