Can I, as the commissioner, draft for others if they don't have access to the live draft room, or their connection drops?
Absolutely -- when you highlight a player during someone else's turn it will say Commish Draft in the box. I have actually done this by mistake by double clicking on a player's name when it was not my turn, so I know this first hand! (You can submit a pick by double clicking OR by a single click and then going to the Draft Box and clicking on Draft Player.
Can you so the same in an auction draft? So If I have one computer up I can enter the auction picks as I go?
Sorry, I've never done an auction draft. Use the Contact/Report a Bug below left, and Hal will answer that question for you.