I do this all the time. If you use the Dual Extrusion Wizard, it will automatically setup 2 processes that are grouped together. That means that the settings that are the same between those processes will stay the same (this video explains it more:
https://www.youtube.com/watch?v=EbQfifnzL4Q). So after it has setup those processes, we just have to go make a single change in Process 1 (knowing it will also get changed automatically in Process 2).
Let's say you want to turn off the second extruder (T1) after layer 100. Open up one of the processes and go to the Scripts tab. Enter the following command in the "post-processing" section at the bottom.
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{REPLACE "; layer 100" "; layer 100\nM104 S0 T1"}
That will turn off the second extruder right at the beginning of layer 100. Just remember to remove that command in the future if you don't want it to automatically turn off anymore!
Note: you didn't say what printer you are using, so the gcode syntax may be a bit different, but M104 works on most machines.