…Continued form previous post.
Select each edge of the not so circular holes and apply the looptools addon, ‘circle’. If you don’t have this addon enabled, you are missing out on some great tools. (BTW this can be done without the addon, but it’s quite complicated)
A little mirror, and subdivision surface modifiers…
This is to show how to make holes in a nonmanifold surface (not solid) If you want to thicken or solidify it you should use these two modifiers to get a clean result around the holes.
I should mention for completeness (and for future readers) that if you have a newer version of Blender the edgesplit modifier can be avoided and instead you can use the autosmooth feature (in the mesh properties) with an appropriate angle. This has the benefit of being able to apply all modifiers and still have a continuous mesh.