If you are using a drill press to put in stitching holes, cut the grove on the back after you drill the holes. This way you can cheat the groove if necessary to keep the holes inside the grove. You'll want a groover that protrudes from the end of the handle like a pen, not the "L" shaped kind to do this . I made mine from a nail, but you can buy one. Making mine allowed me to drill a larger hole in it, so it makes a bigger groove, which helps tidy up the back. I didn't use a drill press though, I bought stitching chisels.
Use a ruler on straight runs if your drilled holes are pretty straight
Better would be to pick up a leather working book that shows how to saddle stitch properly ( Al Stohlman Holster book for instance). You put the holes in with an awl, , one at a time, stitch, pierce, stitch, and so on. This method allows you to put the groove in on both sides first, and steer the awl so that it comes out in the back groove. Much practice is needed, and it is time consuming to hand sew, but it is the prettiest when done well.
I just set aside my stitching pony for a machine a few weeks ago. The time savings is tremendous, but it still looks better when done by hand.
Jake