OP,
I am the one who brought their 10 year old about a week ago.
One thing that I found wierd was that in boarding in Penn station in NY to go home, they don't list the track your train will depart from until about 15 minutes before it leaves. I found that a little frustrating, because I am used to airports where you know the gate HOURS before take off. It's funny to see a mob of people in the train terminal staring at the screen that shows the tracks--then listing gets updated and the mob of people RUNS to the track.

I saw this happen several times while waiting, though not as much for our train. In the end, there was more than enough time for us to get to the train in time--it just made me feel kind of "antsy"--not knowing 'till the last minute, kwim?
If your train will be making all the stops along the way, there will probably be extra seats for your toddler when you first get on...they will probably make loudspeaker announcements telling you that the train is full and to not take up more than one seat per ticket, etc. so if you see the train getting full you can move her on to your lap. In our experience, the most new passengers seemed to come on in Philadelphia, which was about 1/2 way through the trip.