Here's what you will probably run into.
You likely have two separate reservations, because you have adults registered in each room. Each reservation will have separate reservation numbers.
Because your son and his grandparents are registered together in a room, their dining credits will be attached to the key card for that room. The credits for the other group will be attached to the key card for the room they're registered in. Your son's credits will be on a different key card from yours. If your group all eats together, you'll need to present a key card from each room, because your group will not be able to purchase more than 3 meals at once and the other room will not be able to purchase more than 3 meals at once. Indicate to the server whose orders will be related to which key card.
If the party splits up (your family goes somewhere and the grandparents go somewhere), you'll need to have a key card from the grandparents' room to buy your son a meal with dining credits, because you will not be able to buy any more than 3 meals using a card from your room.
If you want your son's credits on your room, you'll have to ask the
travel agent to move him to your room. It doesn't look like there are capacity issues so I don't know why they put him in the other room in the first place.
Credits for the entire reservation will be pooled only if you have both rooms under one single Disney reservation number. It's typical of Disney to give separate reservation numbers to any room where there are adults registered - two rooms will be under one reservation number only if the registered occupants of one room are all minors. Because you worked through a travel agent, you will need to ask the travel agent if you have two separate reservations with Disney or just one.