Basically, you use ingenuity at the end of your Synth (for Byregot's Blessing and your Synthesis Actions) whenever you're level 50 and attempting 1-star or 2-star recipes.
Prior to that, it really doesn't make much difference.

(The math is that you lose a little over 10% of your Progress building effectiveness for every level above you; capping at 5 - there is also a lesser penalty to Quality building)


Rough formulas here (mostly correct)