Quick Answer: With some plug-ins having their own MIDI channel parameters, these also have to be set to the correct MIDI channels for routing to work correctly when playing through Liquid Notes.
MIDI channel settings in Logic and Plug-insLiquid Notes connects to Logic via an IAC bus for establishing the routing connection between both applications. By default, it sends the MIDI events of each track to a separate MIDI channel. In Logic, you have to set the MIDI channel parameter for each track accordingly. Find detailed information on setting up Liquid Notes with Logic in this article - http://re-compose.desk.com/customer/portal/articles/944374-how-do-i-set-up-logic-to-work-with-liquid-notes-.
It may happen that even if you have followed the setup instructions properly you don't hear all of your channels playing through Logic when clicking 'Play' in Liquid Notes. This can be related to a plug-in in Logic that uses internal MIDI parameters and thereby overwrites Logic's settings in the piano roll.
In this case, you need to set the internal MIDI parameter of the plug-in to the same value as the MIDI channel number of the corresponding track in Logic.
Here is an example using Kontakt Player 5 from Native Instruments:
As shown in the image from Logic's piano roll settings above, the MIDI channel of the selected track in Logic is set to the value 2. As output device (not shown in the picture), Kontakt Player is set.
Kontakt Player 5 has its own internal MIDI channel parameters, which need to be set to match this value:
Setting 'Port A (from host)' to 2 matches the setting for the MIDI channel parameter in the plug-in. Repeat this for other tracks of your arrangement, if necessary.
Check your plug-ins documentation to retrieve information about internal MIDI channel parameters!