Carry the lines of the stock straight out on the pad as if the pad were part of the original stock.
Now, doing that is sometimes a bit trying and there are many tips and tools to do that. I've used a 12" disc sander for the last 5 yrs and have been pleased with it over the normal 'garage' sized 6" disk sander. However, I nicely installed dozens of pads for a gunshop with that 6" disk sander.
Some things that come to mind:
-It's important that the sander of choice runs true.
-Use a fresh sanding disk that will cut the rubber.
-plug old holes in the stock by drilling oversize and plugging with dowels and superglue
-layout the new pad holes by finding a centerline then finding where the pad should be located in the vertical position. Keep in mind the rounded heel pads need to located closely to the wood so you don't grind all the rounded area off.
