I recently spent a day banging my head against the wall trying to figure out why Gigabot was not positioning itself correctly during a dual extrusion print. I finally figured it out and learned two important things about Marlin Firmware.
In the upcoming Gigabot Firmware release I am defining the dual extrusion toolhead offset in firmware as opposed to letting Simplify3D define the toolhead offset. The offset distance between nozzles can be dialed in specific for each machine and therefore belongs in that machines firmware. This is especially useful when you are sending gcode to 10 different Gigabots.
Switching control between the two extruders is done using the "T" command. T0 is the left extruder and T1 is the right extruder.
1) The active extruder is saved in EEPROM.
Gigabot remembers which extruder is active even after the power is turned off and that extruder will remain active when power is turned on.
2) Make sure the T0 is active at the beginning of a print when homing Gigabot with the G28 command.
Simplify3D assumes that the local coordinate system for T0 and the Global coordinate system for Gigabot are the same. The T1 local coordinate system is offset about +55mm in the X axis. If you execute a G28 with T1 active all X axis movements will be shifted to the left by 55mm.
Happy Holidays and Happy Printing