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Before you store any tomato based product in a tupperware bowl, you may want to put some vegetable oil or spray it with Pam or something that will keep it from sticking, and therefore you'll prevent staining.
Also, a good tip is to also keep butter and cottage cheese bowls, yogurt, things like that. That way you can store the leftovers in there instead of having to go through and do the dishes. You can just toss them in the trash and it's no loss.