The use of extruders must be configured according to your needs in each section of the configuration. You can select which extruder will be used for supports, filler, brim, raft, etc. If you have generated the profile with the double extrusion wizard, you will see a submenu at the top that allows you to choose which extruder to use (Only Extruder 1, Only Extruder 2, Both). If you select Only Extruder 2 all the settings I mentioned above will be printed with that extruder. The same happens if you select Extruder 1. On the other hand, if you select Both, by default the part will be printed with Extruder 1 and the supports with Extruder 2, but you can change the use of any of them.
When you talk about deformation, do you mean that the support appears separate from the part? If this is the case, it is due to the Tool offset between the nozzles. It will look weird but it will print normal. The same will happen if you print only with the extruder that has the offset, in the preview the part will be seen with the offset but it will print normal.
In my 3D Printer:
If this is not what you are talking about, could you detail what is happening?