Well tbh there's a fair amount of freedom involved, and it also depends what you want to achieve. I could sit down and talk to someone about adjusting gearing for a good 25 mins I reckon, so I'm never going to cover everything in a single post.
I have touched on it in the setup guide, but it's something I do need to explain in a bit more depth when I've more free time.
To actually make this post useful:
Calculation of the optimum shift point is automatic at the moment (well, unless you turn that off) and while worked great in S1, the broader spectrum of torque curves in S2 means it's not that accurate anymore - but at the moment it's best to leave it on, since it provides far more information that using fixed rpm (that way you can only see the drop between gears). Basically while accelerating you want to maximise torque at the wheels, which means stradling the rpm of peak power (e.g. shift at 750rpm above peak power, revs drop to 650rpm below peak power).
*The drop in rpm should get smaller with each gear change, I will add (configurable) auto gear spacing at some point soon.
* You want to be going past peak power rpm in top gear at the fastest point in the track, or acceleration around the track will be less than optimum. How far past peak power rpm depends on how close to the vehicles potential top speed you are reaching (e.g. UF1 at oval, you want to hit about 25rpm past peak power (or some other very low value), FZ5 at FE Club you want to nearly make the engine explode). I will also add auto-calculation of that at some point.
* Make first gear as tall as possible but so the engine doesn't bog down during starts - however this doesn't always allow 2nd gear to be short enough to give good punch out of slow corners (without being too similar in length), so experiment.
Is that enough to start with? More questions, just fire away.