I have a small drill press that I use for drilling. On the table of the press I put a non corrosive container with a slab of scrap rock and fill with water to cover the stone I am drilling.
I drill using the small cylindrical bits you can get for $8 or so on e-bay (Rack of 30 or something)
http://www.ebay.com/itm/30pcs-Diamond-Dental-Burs-Millers-Tooth-Drill-Jewelers-/250867607153?hash=item3a68dfe671:g:vUEAAMXQzr1RzQyoI have a two sided template that I use to mark both sides of a cab when I am doing pre-forms and I drilled a 1/16" hole in the corner so I can mark both sides of the stone I am drilling with a sharpie.
I drill from both sides, half way through, with a one second down then lift, then one second down then lift, repeat until halfway through. Not too much pressure or you will smear the bit or crack the stone. You can see the flour coming off the bit.
It takes me about 6-7 minutes to drill a 4mm hole in the deer sky at 6 mm thick. Other materials longer or shorter depending on hardness.
I drill up to 5mm holes this way with a good success rate. Some bits last through several holes and some do not.
When my hole is complete, I use a round burr to ease the edge. If (as happens often) I have a bit of mis-alignment, I will run a cone burr to ease interior edges
I recommend drilling the hole before you mark out the final pre-form. When it come to breaking the stone, smaller always fractures easier.
I hope this helps...
Bill