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Repetier lets you edit the Gcode, and shows layer your in (i like that!)
For repetier i insert the following code on the layer i wish to color change. Works great for me.

G1 E-3 F6000 ; retract filament
G1 X10 Y5 F6000; move hot end out of the way
M84 E; disengage E motor
@pause print
G1 X0 Y0 F6000; home X and Y axis
G1 E0 F6000; engage E motor