Rover75

I routinely travel between Washington and Boston with a one hour stop over (or longer) in New York using a single upgrade coupon. The underlying fare is the through one way fare. The ticket agents at the Acela Club in DC and at Route 128 in Boston fully understand that a single upgrade applies to two segments of an itinerary priced on a through fare basis. During the most recent triple mile promotion, I used two upgrades on a roundtrip between Washington and Boston with a stopover each way in New York. The ticket price was $314 (two times $157 WAS-BOS through fare) and I earned triple miles on four 750 point segments plus the 50 percent SelectPlus bonus for a total of 10,500 points. The SelectPlus complimentary upgrade coupons allow any upgrade within 48 hours (not 12 hours) which means I can apply the upgrade coupon within 48 hours of the departure of the second train (which means I can arrange a layover in New York for a day or so if I want). I have been doing this for years since it was first explained to me that this was possible by a very helpful woman in the Acela Club in Washington Union Station.

I once tried to do a two segment through fare upgrade by phone and my reservation was completely mangled (repriced in a non-sensical fashion) by an Amtrak reservations agent. In addition, only one of the two segments was actually upgraded. While I managed to get this fixed at the station, I have learned to NEVER attempt this two segment upgrade for a through fare itinerary with anyone other than an experienced agent in Washington or Boston.

To keep things simple, I always book each one way through fare separately rather than as part of a combined round trip reservation.

Also: To restate the obvious, don't you use any kind of restricted fare (14 day advance purchase, AAA discount etc.) if you want to use an upgrade coupon. So, for example, I never use the AAA discount on weekend Acela travel because the three day advance purchase requirement prevents me from using an upgrade coupon 48 hours prior to departure without paying a big fare increase.