My daughter had molloscum contagiosum too. It started out as one bump on her back near her underarm and turned into lots of little bumps in the area a year later. When a whole "crop" of them turned up, my pediatrician sent me to a dermatologist who used cantharidin (which comes from a beetle). It worked miracles, and she hasn't had an outbreak since.
There are several different options for treatment, but the most recommended is to let the virus run its course. Don't pop them (it hurts and just makes the virus spread). Cryo is an option but honestly it's probably not worth the pain and trauma (to both you and your son). Hydrogen peroxide and Compound W don't work, sorry!
I worried about other children noticing them as well, but it turned out that adults noticed them and NOT other kids!!
Don't worry, LOTS of kids get it!!