The only reason for having the mic under the boom instead of over it is if you're worried the screw thread might come loose - that way up it won't turn because it's already at the lowest point.

Mic should be pointing directly at guitar. Most important is which part of guitar to point at - the sound hole is the wrong place because it will be too boomy unless you pull the mic back some distance from the instrument. 12th fret or where neck joins body is about the right place. Other parts of guitar body may work well too but you must experiment to determine if it's any better.
About a foot away, not too close and not too far away, wherever you point it.

If you haven't decided on a vocal mic yet, consider the Sennheiser e835. A Google search will point to lots of reports about how much better it is than the industry standard Shure SM58 at not significantly higher price. I've just bought two and they give a lovely crisp and clear vocal sound.