I agree - more litterboxes are in order. Rule of thumb is one box per cat plus one. 3 cats = 4 boxes. If they have a few really super sized boxes or you scoop several times a day, then you can get away with fewer. If he is afraid to use the box because of the new dog, could you possibly move a box up high for a temporary thing? Perhaps if he's up high and far away from the dog he'll feel more confient.

Cats do not do change well. I'm sure this is a temporary situation for the poor boy!