I recently started traveling with a friend on the NEC and other regionals and discovered a couple of things in the process:
1. It is impossible to choose seats online for more than 1 person. I tried and tried using Firefox, Edge, and my Android phone, all without success. I gave up and resorted to calling an agent and having the seats manually assigned. On an Acela trip, the agent didn't know the right side from the left side of the train and we had to have the conductor move us to the right side to see the ocean going to BOS.
2. On regional trains with the split cafe/BC cars, the Vermonter and Empire service trains that have cafe 'open' (trains that go beyond ALB only, as I recall) as opposed to 'no cafe', BC seats are specifically reserved. For 2 passengers, you'll have to call. The NYP-ALB only trains have no specific seat reservations for BC. It's first come first choice.
I wrote an email to Amtrak detailing the problems with reserving seats for 2 passengers and got the 'form letter' response they are working to improve the online booking system. Yea...they improved it in the past month. I got 'reminder' emails for each of the 2 LD trains I'll be on in the next 2 days that didn't show my current roomette accomodations, but offered an 'upgrade' button anyway. But then, the AVIS rental I've booked has been sending me 'reminder' emails every day for the past week! For what it's worth, I'm currently aboard tr 141 in BC to WAS to catch #51 tomorrow morning.