So, I'll preface by saying that you don't need to: you can oversize the holes for the hex heads, put the bolt in and then fill the gaps with slightly thickened epoxy, job done.
If you do want to hex-shape the holes, this is what I did, and only because I was jonesing to do some woodworking.
1. Use a forstner or paddle bit to drill the hex-head hole slightly undersized, to the depth needed to bury the head.
2. Through-Drill the bolt-shaft hole
3. Push the bolt through the hole and then tap it in so that the hex-head impresses the wood, giving you guidlines to chisel
4. Clean the flats with a chisel.