If using canned tomatoes, do you add to the raw peppers & onions at the beginning, or part way through the cooking of the onions & peppers?

It's entirely your call. As Emiko Davies writes in the headnote, there are different ways of making this dish.

Without a doubt I would start the onions and peppers by themselves first before adding the tomatoes. The former two have flavor compounds that are oil soluble and really benefit from being sautéed. Also, I like the complexity that the Maillard reaction adds.

But do what you think will please your own taste buds and those of your dinner table guests. That's always the most important thing about cooking.

Best of luck.