I have really been trying to figure this out and find an answer to this problem (about 5 hours today...) but I still don't know, how to make ReplicatorG print the support layers with the second extruder I have.

Here is what I have:
MakerBot Replicator 2X with ABS standard filament (right extruder) and ABS support (dissolvable) filament (left extruder)
ReplicatorG with either Skeinforge or Slic3r

My problems:
using Skeinforge: I didnt find any option to build supports and raft using the other extruder - this slicer probalby can't do this... I know how to do dual extrusions, but I really don't want to model the supports myself in CAD.

using Slic3r: I have found the option to print supports with whatever extruder I want (hoooray!) BUT I am not able to find a way of saving a profile from slic3r in ReplicatorG settings - it always uses just the default ones. I tried to generate the gcode right in the Slic3r, but I ReplicatorG told me it doesn't recognise some of the commands.

using MakerWare: 1st) I don't want to use this program at all since ReplicatorG has more options, 2nd) It fails with error whenever I try to export gcode for whatever reson anyway.

What I want :-) please:
Either tell me how to save a profile from slicer in replicatorG
or tell me how to do it in skeinforge
or tell me how to do it any other suitable way

thanks a lot!

P.S.: I tried to use Repetier-Host - which seems to be working nice with Slic3r, but I lack knowledge to connect it with my printer (the program doesn't do it automaticaly as ReplicatorG)