It depends on the gate agent. Last week before my flight to Orlando for work on SW, there was a family of 4 split between the A and B groups. Mom, dad, a girl who looked 10 and one who looked to be 7ish. Mom and dad had B boarding passes and both girls had high As. I was sitting next to them waiting for the flight, and had a B boarding pass not far behind the parents, so I overheard most of what was said. They were told to board two and two or that they could all board with the Bs, but they were not all getting on with the A group. They boarded together in the Bs and had no trouble getting their seats together as the plane was nearly empty since it was the first flight of the day.
Personally, I would approach the gate agent before boarding begins, let them know your situation and ask them what you should do. I feel like they're more likely to help you out or be sympathetic if you handle it that way than if you (general you, not specifically to the OP or anyone else in this thread) pitch a fit when they're actively boarding the plane and ask you to wait until your group is called.
For the OP, The net result is likely going to be the same whether they board together in the As, two A and one in B, or at the beginning of the Bs altogether, it's just that the scenario of you all boarding together in A might not happen depending on the gate agent.