This will be your last step before the guitar is ready to play. The guitar will be fully setup to your liking and in perfect tune, strings FULLY stretched. These are the steps I follow with every floating bridge guitar I setup.
When locking the nut pads you will notice they will twist following the motion of the Allen wrench. The bass side of the pad will pull that string sharp and the treble side of the pad will push that string flat. You can minimize this but getting the pad bolt to just make contact with the pad, and with a smooth "jerk" crank the bolts down to lock, minimizing the amount of twist in the pad. DO NOT over tighten the bolts, it's the easiest way to strip a nut base and will leave you buying a replacement nut! You want the pads firmly tight, just enough to keep the strings from moving under them, you are not trying to crush the string!
With the strings now locked at the nut it's time to "set" the knife edges in the studs. I'll give the trem a real workout, diving, pulling up, usually about 20 times [mostly dives but I want to mix in some full travel pull-ups just to make sure the strings are fully stretched and not giving any more], ALWAYS ending with a full travel dive and letting the bar return to neutral naturally. I'll extrapolate the reason -
It's very rare to find a bridge that will give you 1000% return between diving and pull-up, there will typically be a couple to all of the strings slightly to quite far out of tune [see other sections here if the difference in up and down is too much for your taste] For this reason you ALWAYS want to fine tune after the bar has risen to neutral after a dive [what I refer to as "low neutral"]. The reason for this is typically most players use the trem to dive, and even if you don't, the action of bending a string alone is pulling the trem forward so that if you've fine tuned to "high neutral" as soon as you bend a string you've pulled the bridge slightly out of tune.
You've set the knives and finished with a dive letting the bar rise to neutral. Unlock the nut pads and retune the guitar using the tuners [not fine tuners!] Once you have the guitar back in perfect tune lock the nut pads again using the method above.
Now it's time to fine tune, and with all tuning, the guitar must be tuned perfectly perpendicular to the ground. [using your tuner pluck a note and slowly rock the guitar back toward you [the face of the guitar pointed at the ceiling], watch the tuner and you will see the string go sharp, then rock the guitar forward [the face of the guitar toward the floor] and watch the string go flat. This is the effect gravity has on the floating bridge and why all tuning must be done with the guitar perfectly perpendicular to the ground, negating the effects of gravity on the bridge. [If you're quite round in the middle and the guitar hangs at an angle not perpendicular, you should tune with the guitar in the position it will be played ;)] Without putting any pressure on the bridge [disturbing it's resting spot in "low neutral"], check the tuning starting with the low E through to the high E and adjust the fine tuners on each string until it's in perfect tune [when adjusting the fine tuners it is important to not push down or pull up on the bridge, spin the fine tuners without applying any pressure on the bridge]. Repeat fine tuning low E to high E until every string is in perfect tune.
Plug the guitar in and wail away!