The hinge clearance holes are from the side.
Once I've cut out the rectangular block, I trace the lure shape on the sides, and then put the hinge locations on in pencil. I locate where I'm going to place my weighted hook hangers, and ballast weights, and make them on the lure outline, too.
Then I can see how much wood I have left in each section to put my hinges without running into anything else.
Once I've decided where I'm putting the hinges, I mark horizontal lines, parallel to the bottom of the lure, on the sides at each hinge location. I then eyeball how much back from the marked joint I think the screw eye going to project back from the first section into the second, and mark that point. That becomes the center of my 5/16" hole, which I drill from side to side.
I mark a center line on the top and bottoms of the blanks, and project the hook hanger, ballast, and hinge cut locations up and down, and mark them on the blank.
I then move to the drill press, and drill the 5/16" holes for the hangers and ballast, and the appropriate size hole for the hinge pins, which are located centered in the screw eye clearance holes.
I try to get the holes started straight at the drill press, knowing that, once I've shaped the lure and cut out the joints, I can finish any of the holes by hand, either at the drill press in the case of the 5/16" holes, or while I hold the sections in my hand, in the case of the hinge pin holes.
This sounds really complicated, but, once you've done it, you can make a couple of layout templates for all the joints and holes, and it's simple. Otherwise I couldn't do it! )