Sorry for the confusing title, the best way to explain it is to look at my image (don't pay attention to the lines connecting the holes and sorry for the poor quality)
I have been thinking about this for a while and I can't think about a good way to do it. Booleans would result in a very glitchy topology and very bad results when subdivided, sculpting it wouldn't be precise enough (for me) and modeling it poly-by-poly would probably take forever, not to mention quite challenging.
There is surely a good and simple way to do it, but I just cannot think of one.










