Answers per US phone rep:

Q) Can miles be used ahead of time to upgrade my US flight purchased as United operated by US?
A) No, miles cannot be used.

Q) Does US Airways frequently offer paid upgrades at checkin for less money that buying up to paid first like many other airlines do?
A) US offers paid upgrade by phone within 24 hours of flight but this also cannot be done over the phone due to the codeshare. A paid upgrade might be possible at the airport using the buy up program. $300 per person each way BOS-PHX (not worth it to me at that price)