I do a number of different things when I have to fly with my pack.
If I have pointy things or fiery things that need to be checked (trekking poles, ice axe, used stoves, etc) I will either load it all into a cheap duffel as others have suggested, or put it all into an large rigid suitcase. It really depends on how delicate the contents are. But, these days, I'm finding that I use a rigid suit case more, because it offers better protection, easier to wheel around (as opposed to carrying a duffel) , and I'm paying $25-30 in fees regardless of what I use to check my equipment in. Plus, since everyone UL on this site, it's doubtful your suitcase+equipment will weight more than the threshold 50lbs before additional fees are tacked on.
I usually just place my empty backpack into the suit case, lay my collapsed trekking poles diagonally to fit, and just starting piling in gear wherever it fits.
When my girlfriend and I flew back to CA, she gave me all her pointy/fiery things to put in my suit case, and she went on the plane with her backpack as a carry-on. You shouldn't have any problems placing a 50 liter pack in the overhead compartment.
I think that's the best approach for you and your son IMO. Have him carry on his pack filled with his stuff ( and maybe some of yours), and you check in everything else plus whatever is not legal to carry on.
It's pretty much inevitable that you're going to need something that's considered contraband in the passenger cabin. Namely, a knife, a stove, and/or trekking poles. $25-30 dollars for 2 people isn't so bad. And if you fly Southwest, I think the first bag's free? I sometimes forget to factor in the luggage check in fee when I'mhunting for cheap tickets online...but it's something that you should be conscious of.