I am currently stuck, because I want to cut a series of holes into a mesh I have but I just can't figure out how to do it. enter image description here

Using the boolean modifer only messes up the topology, and I was trying to use alt+shift+s to create a hole using some of the planes. It actually turned out with a good result, but the materials/topology got messed up as seen below:

enter image description here

(I also have a subsurf modifer enabled) I have shared the .blend file, and if someone can figure out how to help it would be very appreciated!