Drilling is self explanatory. Be sure to drill the large holes first, of course. I think a step is an excellent bit to use but you’ll need one that is large enough to make it through at least half of the plywood. Some of the holes are a little snug for the nuts. Use a bolt and washers on the opposite side to snug them in.
Also, take your time drilling. Slowly cutting the surface is better than trying to take out the hole all at once. Remember, there is a sense of fulfillment that comes when we take our time and make things nice!