When you create a new multi instrument and you add an instrument plugin there is a channel to the left, inside the multi instrument window. There you can add audio FX to the inserts and/or sends for that instrument plugin. You can save all instrument plugins, note effects , and audio FX and I believe automation by selecting the top most file icon and selecting "Export Instrument+FX Preset. In addition if you open the main mixer window (F3), you can also add more audio FX to the multi instrument channel's inserts and sends, which are saved when you save the song. Except for automation, I experimented all this using S1 5.4 pro on Win 10 machine. There is more info in the manual (press F1) and do a search for "multi instruments"