Cover the vent hole and plug the thumb as you normally would.  The material will seep up out from the top of the vent hole otherwise. 

After 5 -10 minutes you might need to add a small amount into the thumb hole to replace what went up into the vent hole.

If vent hole is close enough to thumb, I put dam around both and plug both at once. If not, most plug dams come with a solid piece in the center of the cut sizes. I place dam around thumb and pour my plug in thumb then right when plug starts to come out of vent hole, I put the piece of foam over vent hole. This allows air to escape, but put foam (or masking tape) over hole before plug exits or you will not get it to stick.