What I have done to achieve a colour change is to slice the whole print, and then hand-edit the G-code file in a text editor to pause the print where I want to change colour. Just search the G-code file for the characters "Zxxx" where "xxx" is the Z height at which you wish to change the colour. Then insert some lines of G-code that first move the head away from the print (to get the hot nozzle out of contact) and then pauses the print job - find which command your firmware supports, maybe M226 or perhaps M25. Ensure there is a non-printing move after the Z move, and if not put one in to get back to the position it was at before the move & pause. When the print pauses, use your manual printer controls (e.g Pronterface) to wind out all the filament, change filament and wind it in, and extrude into air a few mm until the new colour is flowing, then quickly wipe the nozzle and hit the "resume" button on your printer interface. If you are not going to monitor the print, you could also turn off the hotend heater prior to the pause so it is not cooking plastic in case you don't get to the printer for a while, and you can turn the heater back on manually before retracting the filament.
Example when wanting to change colour at a height of 10mm. Search for "Z10.00"
Section of original G code generated by Slic3r:
....
G1 X83.904 Y63.829 E0.43902 F4200.000
G1 X82.516 Y62.441 E0.13352
G1 X78.628 Y66.328 E0.37388
G1 F2700.000 E-5.00000
G1 Z10.000 F9000.000 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< this is where the search found the 10mm layer change
G1 X130.250 Y69.037 F9000.000
G1 E5.00000 F2700.000
G1 X137.948 Y61.339 E0.37704 F4200.000
G1 X142.474 Y65.864 E0.22164
G1 X140.878 Y67.460 E0.07818
Change to:
G1 X83.904 Y63.829 E0.43902 F4200.000
G1 X82.516 Y62.441 E0.13352
G1 X78.628 Y66.328 E0.37388
G1 F2700.000 E-5.00000 <<<<<<<< Note filament retraction in original code just before Z move
; Manually inserted lines (just before the Z move)
G1 X0 Y0 F9000 ; Move head quickly to park position
M226 ; Pause the print - this is where we will manually change the filament
G1 F2700.000 E-5.00000 ; Repeat the filament retraction as we will have inserted new filament during the pause
; End of inserted lines - note there is already a move that follows the Z lift, so no need to add one.
G1 Z10.000 F9000.000
G1 X130.250 Y69.037 F9000.000
G1 E5.00000 F2700.000
G1 X137.948 Y61.339 E0.37704 F4200.000
Etc.
Dave