I know they are a little pricy, but Rota-broaches work really well, I use them all the time at work, so I have a couple of sets. Clean holes without all the hassle of a step drill.
Me personally, I just went with about 2" up from the first rib. I wasn't too overly concerned with placement as I am going to be recirculating the water in my HLT. I was more concerned with having enough room for my herms coil to sit in there. As far as the boil kettle goes, same thing, not a huge concern for me because I don't have to recirculate through it, I am just boiling there. I did my HLT first and did a test session with it with water only to make sure all was good before I did my BK, that way if I did want to change something, I only had to fix one!! Ha ha
Hope this helps!