If you know all the info for both custodial and non-custodial parent (and sounds like you do) you should input all of that at the same time.
For example, when you run separate NPCs the separate need based grants can’t be added together to approximate what you would get when both parents and your income and assets are combined. Does that make sense?
Obviously, you also would only be able to get one Pell grant, and take one $5.5K loan and have one work-study job (assuming each separate NPC estimate includes both of those items).