We run a V-One RR/Evo - procedure is the same for most cars.
Conventional wisdom says you set droop with the shocks and bar's detached to ensure they don't interfear with the settings. We really only do it this way when the car is first built to ensure there is enough shock length for whatever droop may be required. For the same reason, we get picky about shock dimensions - I want to be able to set droop based on these measurements later. Equally, it's important to have the bars exactly even too.

So, all in all, we use Boomer's Number 2 method for "dynamic" droop, essentially because we need to make changes at the track. We do this with everything attached, measuring the difference between the ride height at rest and when the wheels just leave the ground when the chassis is raised.

As luck would have it, today a fellow racer put our car on his fancy laser tweak station and it was spot on.
To be honest, I was amazed.