The idea is to "stage" your car the same way every time. Driver's preference here. I've known drivers that always "deep staged", made the Pre-Stage light go out (the one at the very top of the tree), swearing that it cut down on their reaction time. I never did, too easy to "Red Light". I always stopped as soon as the Stage light went solid. Once you get used to (with practice) how your individual car "reacted" at launch, you could learn which yellow light to "leave" on.
So in my case, I would do my burn out, then immediately Pre-Stage, and then immediately Stage. Once the "other guy" (in the lane beside me) got done diddle-whizzing around (somehow it became "fasionable" to bunny hop and chirp tires after the burn out, which I was always grateful when my opponent was stupid enough to do that), and actually staged, we'd sit for a few seconds, and the tree would start. I would launch my car on the "second yellow" (normally), and that would have me cutting a pretty fast light (a very short reaction time).
My car would pick up the front tires and "carry" them past the tree. As long as you launched the same way each time, you could factor that into your routine.
And off we'd go.
Sometimes track conditions can affect how "hard" your car will launch (track pavement temperature), if you'd swapped on fresh slicks, or if you changed the air pressure (or God forbid, size) of your slicks, etc. Any driveline changes (gear ratio's, differential, trans, etc) can also affect your car's reaction time. Same with some suspension changes. But once you "learned" your car, (at least mine) stayed pretty consistent.
Also, at the other end of the track, the actual timing lights would be arranged so that the first light you broke the beam on was the one that stopped the timer. The second light, a short distance beyond, was the light you broke that would measure your mph. I always kept my foot in it until I passed the second (mph) light beam. Made for better bragging rights in the pits later.
