Honestly the easiest way to do it is to completely assemble the tower, and using a hoist, lift the tower into the air. Back the boat under the tower, then lower it down slowly until it's where you want it, make your marks on the hull. But since most of us don't have access to an overhead hoist, the best way to do it is to mask up the hull about where the bases are going to sit, and measure CAREFULLY. You know the old saying "measure twice, cut once"? Well in this case I'd measure at least 4 or 5 times to ensure it's perfect.
When I installed my Big Air tower on my old boat, I used a reference point on each side so I had the same measurements and knew it was gonna be square. Width measurement wasn't really an issue for me since I had the tower custom built to my hull width, and it had about 5-6" of play either direction for making adjustments. I started by masking up the whole side from just in front of the windshield all the way past the back of it by about 18", then I started at the the back edge of my windshield where it met the top of the hull and measured downward from the top hull to about center, and then measured forward from that point (using a contractors square to make it easy) until I found a spot that I liked and made my marks. Then measured back from the front mark the required distance for the back legs and made another set of marks. Repeated the process on the opposite side. Double checked my marks and measurements a couple times, and then proceeded to drill into the hull. It came out perfect for me with no play or wobble in the holes with the mounts installed. I actually got lucky with my rear mount, it happened to line up where a factory tower would've been installed and hit the factory reinforcement plate perfectly.
Also make sure to you chamfer your holes to avoid spider-webbing your hull in the future. It's pretty easy and will ensure a long life out of the tower/hull.