I have a {Æther Vial} with one counter, at the beginning of my upkeep, I add another counter to my vial. With 2 counters at the beginning of my upkeep, I activate it to put a {Dark Confidant} into the battefield. Can I get one card at my upkeep?
Nope. All 'Beginnging of Upkeep' effects fire off at the same time to be added to the stack. By the time your Bob is on the board, that moment is long gone.
No because he wasn't there at the beginning of your upkeep.
Nice try:) but nope. Has to be there at the beginning