I've used it a couple times and it's easy! I took it from outside Grand Central, though I assume it's just the same. You can buy your return ticket when you're living so you don't have to bother to buy a one way when you come back home and are exhausted. Just don't lose it
I don't know what terminal or gate it boards at in Penn, but I'm sure it'll be clearly marked on the big time table.
The buses take you right to the front door of your departure terminal. I can't remember, but I think you tell the bus driver or the ticket guy your airline so they know which terminals at which they need to make stops.