I recently purchased a dual extruder and a flexy dually. I’ve used both for some simple tests, but haven’t tried a model that needed support material yet. Warning: Below is just an idea (not tested by me yet…)
I am assuming you already tried the drop down in cura “Support dual extrusion” on basic tab and specified to use the first extruder for support. Perhaps at this point it used the rear extruder for everything (support and model.) Is that correct?
The order you click STL’s for “dual extrusion merge” controls which extruder is used for each STL. So, if the support could be a separate STL, then this would be another way to control which extruder is used for model. But it is probably more convenient to use cura for generating the supports. So I have one more idea.
If cura must generate supports… first, use dual extrusion merge to combine your model with a throw-away model, perhaps a small cube. Click the small cube first (for back extruder) then right click your flex model and merge. If the coordinates of the cube are right, they would be “merged” but still not actually overlap. This order of clicking would tell cura that your real, flex model should be on second extruder. Then, select the drop down in cura “Support dual extrusion” on basic tab and specify to use only the first extruder for support. (So the first extruder would do support as well as the separate throw-away cube…)
Aside: I did earlier do a flex only print, no supports, by manually editing the gcode to switch the extruder activation near the top of the file. I shut off the rear extruder and printed flex only. It printed 50mm forward on the build plate compared to where it “thinks” it is printing, but it worked okay. My backup plan was something like the above idea with a throw-away model which I didn’t test yet. Since you actually do need both materials, I would NOT try modifying gcode… offsets would be tricky, etc… But combining the dual merge order with the drop down to choose your support material should work if my understanding is correct.