I guess my concern is that when booking rail pass tickets there is nothing that pairs our tickets together - other than our last names. Not a big issue for us, but if our names were Smith or Jones…. Maybe it is my inexperience and there is a “secret” way to tie the tickets together.
Since rail passes are sold individually, there is nothing that links them together. I imagine it is possible that if you call for segment reservations with both pass numbers a good agent might be able to put the segment tickets on one reservation number. They might not be able to, too. It really does not matter, though, as you'll see below.
As a couple, it really does not matter. Seat assignment, when it is done at all, is done by the train crew at boarding. If you present yourself as a couple at boarding, you'll be handled as a couple. Bear in mind that boarding processes vary by station, train and even crew. The most common is you simply find your own seats. Some crews will designate certain rows for couples, other rows for families (3+), some don't. Some car attendants have families board first, then couples, then singles, some don't. Other methods are to assign seats at a check-in stand at some larger stations (Seattle used to do this), or assigning seats at the car door at boarding.
Having everyone on one reservation can be important for large parties since they'll show that way on the manifest. Good attendants will see a large party is boarding and will try to set aside some contiguous/semi-contiguous seating for them before their boarding station. But for just a couple, it really does not matter.
You are at the mercy of your fellow passengers and the onboard crew when it comes to seating. What's in the reservation system, beyond a valid ticket, doesn't matter much.
BTW, the Crescent (ATL-NYP) and the Lake Shore (SYR-TOL) operate with single level equipment, so there is no "upper" and "lower" seating. The CONO runs bilevel Superliners so there is. As
@Cal H pointed out the default is upper. IIRC on the reservation, an upper seat is just shown as "coach seat" while lower is called out as "lower coach seat". There are only 12 lower level coach seats and like 72 upper level coach seats in each car. I wouldn't be concerned about getting on the upper level.