In the Shimano reels how do they make the different gear ratios, do they change the pinion gear sz or different amount of teeth on the larger drive gear?

Pinion and drive gear are different. This is the case in all reels, not just shimano.

Main gear and pinions are a set and diameters change. Regardless of brand. 

I'd suggest that the change in speed is accomplished by a combination of both- a change in gear sizes, along with a change in number of teeth on the gears.

To change the speed of a reel, you have to change both the main drive gear and the pinion gear too. They have to match.

Just like changing the gears in a Ford 9" rear.  Replace the main and pinion gear.