I have a vehicle I am re-meshing in order to create all quads. I re-meshed the entire hull already and now must add attachments onto it. In the example below, I am attempting to add multiple view ports to the hull assembly. In order to join the two objects together so that I can begin to recreate the topology, I am using the boolean modifier. Below is a picture of the hull assembly as well as the viewports.
Viewports to be added to hull:
When selecting the hull and applying a union boolean modifier, this is the result:
If I select the intersection, the result is the opposite of this.
Of course, neither are correct as I want to keep everything but the intersection so that I can remesh them together.
I also tried Make Normals Consistent on both objects with no improvement.
How can I fix this so that they can be joined together without having other parts of the model disappear?