I only add nutritional yeast after cooking -- I don't like the way it cooks into things.
Soup is maybe an exception, sometimes, but even with soup, I usually throw in a handful after it's done. IMO, definitely don't
bake the stuff -- I made some kind of a casserole once and topped it with a sprinkling of nutritional yeast before baking, and it was awful. I don't even know why it was awful! But it was. And maybe I'm making this up, but doesn't cooking it make it less healthy for you?
I'd like to strongly second the recommendation of sprinkling it on popcorn. We're addicted to it in our house. I actually travel with a small container of it when I visit out-of-town family, because usually we're making popcorn and somebody says, "hey, Comtessa, do you have any of your magic popcorn seasoning?"

I also frequently sprinkle it on top of steamed broccoli (magically convinces 16 mo DD that broccoli is edible -- I have no idea why it works, but I ain't arguing), vegetable stir-fries, and grain dishes (like rice pilaf) that need a little 'livening up.'
OP, I'd suggest sprinkling it on your quinoa
after heating, as a condiment. A good rule of thumb that I use for nutritional yeast is, I put it on anything that I think would be improved with a sprinkling of Parmesan cheese. Similar enough texture and flavor for that to work, most of the time.
My grandmother used to make a drink she called "tiger's milk." It was milk mixed with generous portions of molasses and nutritional yeast and I
think a raw egg, too. (It was 'tiger's milk' because the molasses made it stripey -- get it?) We all had to drink it -- children and grandchildren alike. It was truly dreadful, but I'm sure it was healthy!
p.s. I LOVE the crispy-fried tofu from red + lulu!!! I'm going to try that tomorrow for dinner!!!