On My D7100 and 105 micro lens, I start by setting my camera to ISO 200, f16, 1/250 for flash sync, exp comp +3.0, I put a diffuser on the end of my lens for the onboard flash, similar to what Scott uses.
I check how the shots look on the back screen as I am going, I find I dont have to change much from that, I would rather my shots were a little on the dark side, easy to lighten them up a bit in PP.
I think if you start by using those settings, and check what they look like on the back screen as you go, and make changes on the go if need be, you should be off to a good start.