NOT the extruder output, the hotend output.
NO you do not tell your system to turn up the second hot end, the programing is setup so it has NO second hot end.
The programing is aware the fan is on the second hotend output and when you say 'Fan on" with M106 it will put power to that output expecting a fan connected there.
If you try to turn up the second hot end with an actual hotend command like say M109 S200 T1 (set hotend #T1 to 200c note the first hotend is T0) it would return an error because its configured as ONE hotend so T1 does not exist.
Now, there are differing ways of distinguishing extruder etc. In my book an extruder is a stepper motor mounted to a system to push filament at a specific rate.
A hotend is the place where a heater and a thermistor work together to keep a specific temp to melt that filament and using the feed pressure supplied by the other part (extruder) apply it to the layer at hand.
In some cases you have to distinguish how people communicate about these two functions (that work closely together) as I constantly see things like "what temp should I set my extruder to?"
Extruders FEED its a motor! They don't have a temp setting!!
Its a pet peeve
might just be me....