If your son is going to be going as a lap-child, preboarding really won't make any difference, except perhaps to keep them out of a middle seat. He might want to consider skipping the preboard if the flight is not completely full.
Here's how I would work it: If he's lap-carrying the baby, I would advise having him checkin online to get an A, then just boarding at the back of the A's unless the flight already has passengers on it when it comes in (the gate agent can tell him if that's the case.) He normally should not get stuck with a middle as long as he's on by the end of the A's. The reason why I would do this is to maximize the run-around time that squirmy lap-bound toddler will have before he is forced to sit still for hours. If DH gets a B or C pass, preboarding will be much more advantageous, but it nevertheless means standing in line longer for the preboard, and having the little one trapped on his lap for a longer period as well.
If DS is flying in a carseat in his own seat, preboarding is not only desirable but necessary, because of the limited options for placement of the carseat. However, if he's lap-carrying, staying out of the plane that little bit longer will help some with the squirmies.
