I never use booleans if I can help it.

I use the Insert Edge tool to "draw" squares where the circles are going to be, then extrude the squares created in a bit, then a bit more, and finally a tiny bit more.
So I extrude them 3 times inwards. Then I smooth the object, which will turn the square holes into circular holes.

I extrude three times to keep the shape sharp.

If it's a small hole (like an indent or something), two extrusions would do it fine too.