So I went for the westerly mileage upgrades, confirming on BOS IAH and waitlisting on IAH SFO. Here is the fine print presented to me:
Important Waitlist Terms and Conditions
Immediate redemption is required. The service fees and mileage deduction for all OnePass upgrade rewards will be assessed at the time of request. If you change your mind and would like to redeposit your upgrade reward, your fees and mileage will be refunded upon payment of any applicable reward redeposit fees.
What happens when waitlists expire? At 24 hours before departure, any waitlists that did not clear will expire. Upon check-in, however, you will automatically be added to the airport upgrade standby list for any flights that were waitlisted. The airport upgrade standby list will be cleared by a Continental airport representative at the gate once the flight has closed for check-in.
What happens if your upgrade does not clear? For BusinessFirst upgrade rewards, all miles and service fees would be refunded, without a fee, if the BusinessFirst segment of the trip could not be upgraded. For all other upgrade rewards, miles will be refunded only when no segments of the trip could be upgraded. When applicable, service fees and miles will be refunded 7 to 10 days after the trip.
How are waitlists prioritized? Waitlists are prioritized based on the Elite status of the OnePass member who redeemed the upgrade reward, followed by the time in which the waitlist was requested.
Note that this is "one size fits all" description of the waitlist. It does not address how to handle my situation, where one leg has cleared and I have now paid for both legs. By implication my position is no better for this reason, but the existence of a PR-1 list offers an alternative way to handle this.
I made and cleared a PR-1 list once before, changing flights on the domestic leg of an international BF award. I changed at the airport to the flight I would have booked had it been available, to avoid a forced stopover. So some parallels, but a different situation.
Edit: I realize that a phone call is weak evidence, but I spoke with an agent that sounded quite versed in these details. She asserted that once one segment of a mileage upgrade clears, I automatically make the "PR" list for the remaining segment. Same with a misconnect; I make the "PR" list for the new flight.