I don't actually fit minus molds inside holes way back as it is so easy to just glue it above the surface. Looks very amateur though and fitting minus molds inside holes looks way better.
It is actually simpler than how it looks. You need the proper tools and you are good to go!
Basically you need two sizes of drill bits. The first bit should be smaller than the mold itself. In fact the first hole is just to guide the bigger drill bit soon after.
The second drill bit is important! It should be bigger than the minus mold so that the mold will fit snugly inside. The trick is to NOT drill all the way through. A rusted old bit is perfect for this task rather than a sharp new bit.
The photos and this tip is for small kotobukiya parts or minus molds. For bigger molds the concept stays the same but is a bit different in a way.
Hope the photos below explains it better...