Yep, they can get it in only one eye. Not sure how you'd prevent a case of it... Good thing you had it checked, though, since I believe it's like pink eye in kids--contagious.
The vet might be able to give you advice on how to prevent a recurrence.
I hope he responds to the meds quickly.
Any chance of getting a picture of your furbabies?
We'd love to see them!