TouchOSC is a very good, cheap option. V-Control Pro is the most expensive, but a pretty good WYSIWYG option. There are some Lemur templates to control Logic synths which I absolutely adore.

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.

You can use the Remote with Bluetooth, too. it's a much stronger connection. Just be sure to pair the iPad and the Laptop. Then turn WiFi off before launching Logic Remote. That way the remote will only connect via the Bluetooth.

I really enjoyed the original music theory series and got really excited today to see the Jazz additions. Thanks so much!