[Stiglr]

Well, the simplest way to make a circular hole in a rectangular surface might be to do this:

1) Create a polygon of the proper shape and size you want your circular port. You'll use this as a visual reference.

2) Select the surface in the hull where you want to make the hole.

3) Surface Mode.... Surface \ Make Hole. This will create a hole of the same shape as the surface itself.

4) Now, in applicable Ortho view, orient your reference porthole shape in front of the hole you created with the Make Hole function.

5) Going to Vertex Mode, select Pairs of vertices and if needed, Vertex / Add Vertice to create extra vertices in the sides of the rectangular hole; your goal is to end up with the same number of vertices in your hole as you have on your visual reference. Drag the vertices to their proper places in the viewports, taking care to align them in all three dimensions, so you don't distort the hull you're creating the viewport in.

6) Once you're done with one hole, use the same visual guide poly for the others, and when you're completely done, Edit\Delete the visual guide.

A more complicated way would be to use Booleans to cut the ports, but this could (I predict: WILL) wreak havoc with the original hull, and explode poly count way past where it would be useful.