Hello @Lrbllngs
Thank you for contacting the Instructure Community. We're sorry to hear you've been experiencing issues with averaging grades. As of now, there isn't really a built in feature for this but you do have a couple options - both require some manual moving around at the end of the semester. You could move assignments you don't want counting towards the final to their own assignment group worth 0% then at the end, move them into their respective groups. Additionally, you could leave the assignments in the groups they need to be in, and under edit enable the "do not count this assignment towards the final" However, you'll want to keep record of which assignments you switched and then switch them back at the end.
If you need to average out the scores for 3 assignments until a student reaches a particular percentage - then make one not count, etc. that unfortunately needs to be also done manually. Canvas has a way to drop the lowest score in an assignment group, but it doesn't really help with tallying up an average first. Hopefully this information helps.