Make the big holes too. Just adding lots of small holes aids in the water exchange which will aid in making sure there is enough DO inside the structure to make it comfortable for fish to use. Varying sizes gives lots of choices from everything down to the level of algae on the surface all the way up the food chain to whatever size fish you are trying to protect. Let the biggest holes be the size fish you want to allow some protection to. Smaller fish can dart either side of the opening to escape predation. But if you do not get enough water exchange capability the center of any structure might not get used much.
Some of my smaller structure pieces I think I did not get enough larger holes in. I should have used a jig saw like you did.
