Secondary Fuel Rail?
 

How can you tell if it is seated properly without taking the whole thing apart again?
Does it make a difference if you put the grommets into the ports then the rail or do you place the grommets around the injector body before putting it in the ports?

You should be able to look at the injector tips and see a nice even, but very narrow gap around the seat in the intake. As to your second question, place the "grommets" in the seat opening first.