You will get points for the Family room, the van's fare, and your railfare. If, and this is important, your wife is listed on the reservation as the second person then she should get points for the roomette and her railfare, assuming that you provided her AGR number. But you have to have provided her AGR number if you want her to get the points. So if you didn't do that, then yes, it's time for another phone call to AGR.

Don't worry if the ticket actually shows her occupying the room, the attendant won't care who occupies which rooms, again assuming that you're all in the same car. If you landed the roomette in a different car, that could be a problem. So if you didn't already confirm this, make sure that you have both rooms in the same car and I would make sure that you got a room number in the 11-14 range, which means that you have a roomette downstairs by the family room.

And yes, since you needed two different types of rooms, the only way you could have booked this reservation easily was by phone.

It was probably a good idea to get the second room, because unless your 13 year old son is very short, he'd probably be rather cramped in the child sized bed.