Typically, yes, it's easiest to wait until the Notice of Assessment has come back before making an adjustment.
It's a shame it's only a few days before the tax deadline. If you had more time, you could have had him prepare another return with all the right amounts and simply not file it. Then you could get the amounts you need for your return. With our online editions, you could prepare this second return at no cost.
Instead, the best option to avoid a mess with the CRA would be to file your own return without the benefit of his tuition transfer amounts and then make your own adjustment when your son makes his. If you were expecting that your son's tuition transfer would reduce your tax payable, it means you'll pay a little more tax by the deadline but will get some money back when you adjust your return.