You don't have to do anything special at all. Empty the bag normally; you'll probably want to do this before the flight just because it's easier in a bigger toilet. When the bag is empty, it's, well, empty - there is a little air in it but no significant amount (if in doubt, just press it a bit with the drain valve open, then close the valve). That's it.

When you're flying, just deal with the bag as you normally do. As I said above, though, you might want to monitor his position a bit as it's easy to get the bag and tube twisted (if it's a leg bag anyway) so it's not draining well. All that means is that the urine doesn't drain from the bladder, and will do so rapidly when the tube is unkinked.

Have a good flight and don't worry (much) about it

A 6 year old probably won't be going through the body scanner so they won't even know he has a bag at security. That's nice.