No worries taking a bit of media from your son's filter to help your other tank. Ultimately, fish keepers have been doing that for generations to seed new filters. Just be glad that you have that option. It's far more reliable (and WAY CHEAPER) than any "bottled bacteria" and it is guaranteed to have cultured bacteria and with no real change to their environment, they probably won't even slow down in their processing.
Just be sure to replace the borrowed media with new stuff so that it can be recolonized. These colonies can double in 24 hours, so in theory you could take half of the media without a major problem. In practice though, it is recommended you limit your borrowing amount to no more than 1/3rd. If you are worried about a spike in his tank (it shouldn't happen) just don't feed that tank for 24-48 hours. They will be fine.