I think this can be done using the support alteration files. In the raft option, you can specify a start and an end file. The simplest would be to enter T1 in the start file to specify the second extruder, and then T0 in the end file to go back to the first extruder. At least, this is my understanding or the reprap firmware and gen 3 electronics with the extruder controller. This might not be true of other firmware.