FlexyDually Issue

I just bought the V2 Flexydually for my taz 5 with the idea of making parts out of ninjaflex and having ABS/HIPS as support. However all i can seem to do is make everything out of T0 (plastic) or make the part out of plastic and have the rubber (T1) be support. Is there a way to make the second extruder (T1) the primary extruder? Thanks

In slic3r there is a setting for what extruder to use for infill/support/perimeters.

In Cura check out support Dual extrusion, that may give you what you are looking for.