3dUni is the right place to be looking for FF advice on setting up Slic3r. For Slic3r getting right, left or both extrudes to work on a given print is all about you custom start gcode. (One of the things that I dislike about setting up Slic3r and why I have been looking at Cura and KISSlicer.)
Gcode you need to check for your heads are these lines. M104 and M109, it looks like you already checked M109.
“M109” is your heated bed temperature. “Tx” is your tool head; “T0” right, “T1” left. For the bed you should use “T0” when you are printing with the right head or dual heads. Otherwise use T1 for the left (seems like you probably know this though)
“M104” is for heating your tool head you are going to use. S[first_layer_temperature_0] is you right heads temperature and S[first_layer_temperature_1] is for your left head… and Tx is the same as above.
So if you have this line in your gcode: M104 S[first_layer_temperature_0] T0;
You need to change it to this for the left head: M104 S[first_layer_temperature_1] T1;
For printing with dual heads you would add both lines to preheat both heads before printing.