With Ai lenses you only have aperture priority, so no dials needs to be used, only the aperture ring on the lens.
With non-Ai lens the back dial is used.
I had been using a modern non-AI lens extensively the past couple of weeks and that's why I was confused. This lens doesn't have the AI ridge but also doesn't need the metering coupling lever to be flipped up. With an AI lens the aperture can be controlled from the lens, and that resolves most of my concern on this issue. Thanks for the correction.
For a non-AI lens, after adjusting the lens aperture then the front dial ("sub-command dial") is used to adjust the camera. This is on page 167 of the manual. The rear dial ("main command dial") normally has no effect on aperture. However, menu item f7 allows for the two dials to have their functions switched. I just noticed there's also a setting available under that item where the main command dial controls aperture only in exposure mode A. This seems like it will work really well for avoiding the front dial.