JayBee: to measure droop you can actually probe anywhere you want as long as it's always the same place. People use differenct measurement spots: below king pin, below C-hubs, below A-arm... it really depends on racers' habits, so when people fill-up setup sheets they should actually indicate where they made the measurement! Personnally I like to measure it below the king-pin... it's the easiest.
Measuring it with or without shocks should yield the same result, since it's the droop screw that limits A-arm travel, not the shock (although some people still use shock length to control droop, a method which I don't like). However... it happens sometimes that shock shafts "stick" to the O-rings, distorting the readings (the A-arms don't "bottom-out" like they should). Here's how I do it.
1- Unhook the lower shock retaining screw.
2- Make sure the A-arm is as low as possible (droop screw hitting chassis)
3- Adjust droop with droop screws
4- Make sure that, when fully extended, the shock bottom is lower that the mounting hole you want to use (so that it's still the droop screw that limits uptravel)
droop is a tricky thing to adjust and measure... because it's closely related to ride height, tire diameter, C-hub position, etc... the most important thing is to make sure it's symmetric, and that there IS some droop on your chassis (so that the wheels don't lift the ground as soon as you lift the chassis, in order to soak holes on the track and keep the tires on the ground in unloading situations)
PS : sorry if my english is not 100% clear... I do my best