well it has to be applied to the instrument at all time, but it does not have to be active
In computers 'active' is denoted by a set-bit or '1'
Inactive is '0'
That is know as a 'flag'
In lmms you can set all flags to ON with '1' and OFF with 0, in automation!
So every diode with light is a '1'
Every un-lith diode is a '0'
Drag any diode into automation-tracks, and set the 1 or 0 as you like, and the effect or plugin will change on/off state accordingly.