I am making holes in my mesh to put tubes inside. The problem is that it doesnt work well with subsurf. I know one way to fix it but it changes the shape too much. I have made a video to show what i am doing. Hopefully some can provide diferent ways to do it. I have tried boolean mod but it turns out the same way.
A couple of things you could do differently that will help...
- Apply Rotation & Scale before going into Edit Mode. That will keep your use of the Looptools > Circle from creating ovals.
- Add an extra vertical edge loop in the middle of each section where you plan to put the holes.
- Add an extra horizontal edge loop that cuts across all three hole areas.
- THEN start doing the extrude/scale operation(s), followed by use of Looptools > Circle to create the holes.
Doing it this way will give you eight-sided holes which work out better in the long run.