Open apple-L is the logic Midi learn command. I had the same problem with mapping the same knob to different parameters. The trick is to tweak a digital knob, open apple-l to go into learn mode, twist the physical knob, then open apple-L again to exit learn mode. then repeat with a different knob. hopefully that should work for you.
If not, the other way to do it is to setup a monitor-transformer-monitor system in the logic environment which I find can be helpful in making sure that one knob is always affecting the same thing by transforming from the knobs control change info to match the digital control change info, but it's more labor intensive and takes more time, though it is pretty exact in its control.