Those gauges are meant to be used two ways. One, to check the radius on a neck as you plane the surface, or to identify the radius on an existing neck. The other use is as an under-string gauge. Assuming you have adjustable saddles, you can match the string heights to your neck. They really only get you close - you invariably have to tweak the saddles a bit to get things perfect. But, they do speed up setups a bit.
What you're asking to do is unusual. To answer your question directly, the 16" gauge is the one to use - under the strings. But, that's not going to flatten out your strum trajectory. If you want to do that, you're better off with the depth probe on a dial caliper, and adjusting the saddles using the body as a reference. It would be a weird setup, though. Your E, A, B and E strings will end up unusually high once you get the D and G strings set right.
I've never heard of anyone doing or asking how to do this before. Are you coming from a classical guitar background? Those are often flat necks, or very close to it. Still, adjusting to the radiused neck usually isn't hard to do, and happens quickly and almost automatically because it's so much easier.
