I always use dill-aid .ulp because it gives a center-punch effect, which makes drilling by hand much easier. That is, the drilled hole will be centered in the pad. It is similar to using a center punch when you want to get a drill started correctly on a piece of metal. If you are using a CNC drill it won't matter.
Drill-aid.ulp uses layer 116. You could run the program, then show only layer 116 and delete half of the small disks. Then proceed to make your PCB pattern. That way, you can find our whether partially filling the pad holes helps you. I forget what the default diameter drill-aid gives. You might just use the default at first or something like I recommended (0.5 mm). If it is too small, then the hole won't etch and you lose the effect of having a center punch. If it is too big, then it doesn't guide the drill's point. Something about 1/2 the diameter of our drill should be OK, if that is not too small to etch.
John