All 40 players count against the cap in the base game - some of the owners who have been around for a little bit longer have come up with some custom rules around this, but every rostered player gets paid in the base game.
I’d definitely start with the FAQ tag:
And specifically for the auction draft:
Once you get the beats of the game, which doesn’t take very long, Ottoneu is not to understand. It is pretty hard to master, however!