Well I got back on a trip to Panama a month ago and I was on Malarone. The side effects did not seem to be very bothersome and having them with a meal in the morning seemed to work fine. However, I cannot be certain what happened, but on my way back I was flaring up. I don't know if it was the stress of starting the trip, getting the vaccines (Typhoid, Hep A & B, Tetanus), less control over the food I ate, or who knows what. I also noticed I may have been flaring before I left and only a week into the trip on the way back home, it got much worse and I apparently didn't pick up bacteria or parasite.
So I don't have a good answer with all of the above and the Doc will probably say it isn't an issue. I'm inclined to agree for some reason and the research I did on Malarone didn't seem like it was going to be an issue, as far as I could tell. If he needs vaccines, it would be better to spread them out, I'm thinking. Hope this helps and hopefully you both with have a good time.