You don't want any bulb in direct line-of-site with the windows of your house, or your primary sitting area when out by the pool. The glare from a pool light can be annoying, and not nearly as nice as a pool lit such that you don't see the bulbs. I think one of your position 3 lights would be a problem.
I think two lights are the way to go, especially if they are color-changing LED lights, which don't provide the coverage of white incandescent or halogen lights, especially colors in the red spectrum. If your primary seating area is between pool and house, I would go with the right hand position 1 (full sized light) and right where the lower-left arrowhead of the dimension line labelled 16' touches the side. That would give you one at each end of the pool, both shining away from the house.
Position 2 lights would also work, as originally spec'd. A lot depends on where your primary seating area is. The left-hand position 1 light will not cover the deep end very well, IMO.
I would ask them to "home-run" the wiring from EACH light back to the pad (or wherever the light switch will be). This gives you the option of wiring all three lights together, on one switch, or wiring each light to its own switch. When kids are in the pool: light it all up. But for a nice romantic or ambient lighting affect, it might be nice to have just the spa on (or off!), or just one or two lights on. Running the wiring now leaves you the option to change your mind about the switching configuration in the future. If they're all wired together out in the yard somewhere, in a J-box, it might be difficult or impossible to change that up later...