Without getting involved in the complexities of setting up suspension, pre-load has one very simple job.
It's there to ensure that the shock is within its correct operating range, so that it neither tops out nor bottoms. With rider and bike supported by the suspension it should have an amount of sag equal to about 1" or 1/3rd of its operating range. The fact that it does alter the ride height is no relevant. It should not be used to alter the ride height, although many riders do use it that way. Neither does it alter the spring rate.
If you're riding on roads smooth enough that the full operating range of the shock isn't used you can use pre-load to tweak ride height a little, but that isn't its intended use.
By altering ride height at the rear you're effectively altering the steering geometry - the head angle and trail. That's best done by adjusting the front fork height, keeping geometry changes and suspension changes seperate.
So with preload (sag) and steering geometry set, you can then play with the real suspension settings of damping and spring rate (but altering spring rate - usually be replacing the spring unless your forks are air assisited) will require re-setting the sag.