I marked the holes by putting a dowel center in the end of a long piece of 1" dowel. Run it through the holes in the base plate, and bang on its end with a mallet. Rotate it a bit and bang it again, and repeat. Odds are the dowel center won't be precisely in the center of the dowel, so you'll be making a small ring of marks. The center of the hole is, of course, the center of that ring.
I agree that even at 12x12, things'll be "cozy" inside. That's OK. Keep in mind that this will be a general purpose hobby shed, not just a wood working shed. Even 12x8 would be plenty big enough for building 1 meter wingspan bungee launched RC gliders. And for the electronics projects I do, I only need enough workbench space to do some soldering with a 3rd hand (for electric guitar pedals). If I need more room than the shed offers for wood working projects, I'll just roll the table saw down a ramp and do my cutting outside in the sun.
Our Lexington model was designed to match many traditional New England homes, in Massachusetts and beyond. The steep pitch of the roof is built to withstand sometimes-punishing New England snow loads and complement today’s home design styles. Post Woodworking can match most vinyl siding colors, so that your shed color will coordinate with your home as well. And as is the case with all of our sheds, interior solar lighting is available to light up the night.