Did you define your external MIDI device in the environment? That is, create a new multi-instrument and enable its MIDI channels so Logic knows about it?
Regarding the channel strip order on the mix screen, the mixer and the arrange window tracks are (by default) linked. It you change the arrange window track order, the mixer will reflect the new order. If you open a separate mixer window (I use dual monitors for this...), you can also have the separate mixer window display a different track order (than what you see in the arrange window). That process requires activating Logic's "H" or "Hide" button. Activating the "H" button (in the local arrange window) adds another button to each track (similar to the "R" "S" "M" buttons). There are two levels to the "H" button, but only one is visible if you are only using the Mixer at the bottom of the screen (integrated below the arrange window). If you have a separate mixer window open, the first time you click the "added" H button it will hide the corresponding track in the "independent" mixer, but leave the tracks in the corresponding arrange and "integrated" mixer windows visible. When you click the "master" H button, the tracks will also be hidden in the arrange and integrated mix window. Useful if you have more tracks than will fit within your screen real estate.