Should I use onions that are not so pungent?
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Probably a question you'll have to answer for yourself, but if they're regular cooking onions you're probably fine- some of the wild onions can be a bit much. You might want to use less than otherwise, or consider something like Marcela Hazan's recipe, where the onion is cooked with the tomato and then removed. Did you cure the onions? It's usual after picking to air cure them for several days- usually they're just left atop the ground for a while. This dries out the outer layers and tones them down some.
You can also tame onions by soaking the sliced or diced bits in icy water for 20-30 minutes. That soaks off some of the chemicals which give onions both smell and bite. Taste a bit after soaking, and decide how much of the onion you want to use. Also keep in mind that most onions do mellow in the cooking process, which also removes a lot of the strong taste in favor of the sweeter ones. You could saute your onions, a small amount, to see if this would hold true for yours. The soaking trick is useful in things where the onions will be raw, but it works well for those you will cook as well.
I would use a less quantity of the onion called for in the recipe- maybe resuce by 1/3- and saute it first at a rather low heat for a good long time - they should be almost falling apart. This should temper any overwhelming flavor