Hi,
I am trying to get the mounting holes covered in the copper pour but I am not sure what would be the best way to do that. Is using the shape edit to manually edit the shape of the copper pours the only way? Any advice would be appreciated.

 

Is what you are looking for to just form a pad with the bare copper exposed? If so you may make a pad as a mechanical component and add this.

Alternatively if you are aiming for plated through holes then you must define the plating in the padstack editor.
Remember you may call plating thickness out in your fabrication notes.

Perhaps I don't fully understand what you are trying to do by covering the mounting holes with exposed copper, would you be able to provide more details as to what the goal is here?