Different speed for Magic Mouse and built-in trackpad
In my testing just now, the trackpad and mouse have separate tracking speeds. I moved the trackpad to the slowest setting, and the mouse to the fastest. The trackpad was slow and the mouse was fast. The two did not seem to affect each other.

The answer should be to move each to the setting that works for you. 

Could you elaborate more on what happens when your adjustments affect each other? Have you tried setting each to a different extreme to see what happens?