Andrew Smith, I've had this same question since our college converted to Canvas. See this feature request for the most recent one:
I still can't believe that we can't set our courses to grade all by percentages and then average those percentages together instead of adding all points and dividing for the entire semester. I think it's a lawsuit waiting to happen.
But for now the teachers (Those who have realized Canvas doesn't average the way they expect) are using the method described by Chris Hofer: Make everything--assignments and quizzes--worth 100 points. I have a google doc spreadsheet that I use to manually convert every assignment or quiz into percentage that I can then enter into Canvas. It's kludgy and requires extra steps, but it's the only way to accomplish this for now.
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