This is doable, I think you might just be a little mixed up with how the software works, so I'll make a list to keep things simple and organized
I'm gonna assume that your ABS is in the right extruder and PVA in the left for my instructions. If it's the other way around you just have to be smart about it when you follow my instructions, but that should be pretty intuitive.
1.Import model
2. Edit Process button
3. Select profile- MakerBot Repliator 2X (both extruders)
4. Auto-configure-Select ABS (it defaults to this)
5.In the layer tab, make sure it says right extruder, in the infill tab, make sure it says right extruder.
6. In the support tab, select the check box for "generate support material", then choose the left extruder.
--So not we're at a point where the print is setup for a dual extrusion with the right extruder printing the model and the left extruder printing the support. The issue is though that the software is set for ABS- so your extruders are gonna be set at 230 degrees Celsius, which is a bit high for PVA.
7. To change the temperature of your left extruder, go to the temperature tab. click on the left extduer in the "temperature controller list" and then remove the Layer 1-Temperature 230 setpoint. After you've removed it, you can add a Layer-1 Temperature 190 setpoint which should be good for PVA.
8. Make sure that this process is on the model you'd like to print by using the select models button
That should work