Hi Donny,
As you may (or not) remember, Yamaha PSR keyboard's don't store setting after you turn the keyboard off, so you need to first create & store (in the PSR2000's USER Reg area) a custom Registration Memory file which includes your prefered pedal settings.
Once this is done, everytime you boot up the kb, you'll need to remember to load this Reg file. This might seem like a hassle at first, but trust me, it will quickly become second nature.
Scott