Since switching to Canon about 8 years ago I've always had the top dial (next to the shutter button) as shutter speed and the rear dial (next to the screen) as aperture. I believe this is the Canon default. It's also the way that my Canon EOS 100QD film camera is setup.
Since buying an RP, I still have the shutter speed on the dial closest to the shutter button and aperture is on dial to the rear of the top panel, which is actually a really good position because that's where my thumb rests next to the AF on button that I use for back button focus. The RP doesn't have a dial next to the rear screen.
To change ISO, I press the M-fn function button and use the dial to adjust the ISO quickly.