For start with correct extruder you have do this:
from the settings of the 3d printer just copy the original start and end gcode from kisslicer, and at the end of the start gcode just add T0 or T1 or T2 depending on the extruder that has to start printing. For example if the print starts with a raft with HIPS on extruder 3 add T2 at the end of the start gcode. I have a 3ntr printer with 3 extruders and everything works fine with cura.