Be sure to call the AGR phone number instead of the regular Amtrak(Julie) number. When I call AGR(usually a few months in advance) the AGR reps are friendly and let me make specific room(and car if important) requests as part of the booking process and 99% of the time my requested room is available. I stopped making on line reservations over a year ago. Only drawback is that your reservation is not listed with the on line bookings but you can still on mobile apps pull up your reservation and save the boarding pass in IOS in the Wallet App. Also you can save a photo of the PDF boarding pass on your phone.
PS - I found during recent travel that Amtrak Reps are much more supportive than Via Rail Reps. On a recent trip especially in the Toronto - Montreal corridor Via Rail changed Business Car equipment and seat assignments without any notification. When I ask for help reassigning my seat I was ALWAYS told car was full and I could not change my seat. What was distressing was that I had reserved a seat mid car and was move to the third row over the trucks. Across from me a couple was surprised that they now were sitting at a table riding backwards facing another couple they did not know. When I discovered that a third trip I had booked on that corridor route had been similarly fitted with substitute car and I was back in the third row in a 2 -2 car instead of 1 - 2 LRC car I was informed not a thing I could do about it. So, Instead of traveling to Montreal to visit for a couple days, I cancelled that train and stayed in Toronto 2 extra days and took Amtrak's Maple Leaf business class back into the USA from Toronto instead of the coach only Amtrak Adirondack from Montreal.