Rear-end Gearing does one thing. It moves the sweet spot of the engine's power band. If you need that sweet spot at low speeds you go for lower gearing (numbers above 3.70 usually). If you need that power at high speeds you get higher gearing, number in the sub 3.55 range typically but not always. It depends mostly on the type of engine you have.
The tranny ratios simply try to keep the shift points coming at the point the engine starts to nose over. The next gear should keep the engine in the sweet spot. It gets way more complex when you have to figure in partial throttle operations, and the like, but this is the simple explanation. What also makes things tough is the engine management system calibration along with ABS, ESP, and LMNOP. The heavier 20" wheel/tire combo takes a bit more power/torque to get moving so the lower gearing keeps the performance number where they need to be. Plopping SRT8 20's on an R/T probably throws all the electronics out of whack. Significantly changing the wheel/tire from stock requires all kinds of adjustments to keep the system optimal. This also contributes to people snapping drive lines while drag racing with their bling'bling 24's on
