Yup, Dan's method is a good way.

Other modelers have a tool called an N-Sided patch that can also be used in this situation - MoI won't have this tool for V1 but I hope to add it in the future to help with capping more irregular holes.

Another thing that can generally work is instead of making an irregular opening at the top like that, model a top sheet with a sweep or something and then trim those parts with each other. That way you are more explicitly controlling the shape of the capped surface, rather than trying to cook up something to follow a wiggly boundary curve.

- Michael