Run GCS.
Plug controller (Revo, CC3D, etc.) into USB and wait a few (10) seconds for it to see the controller.
Select Configuration tab at the bottom of page.
(Within Configuration tab) On Vehicle page, configure an accessory like Accessory0 onto some output (like say Output #6 which is the last servo connector position on the controller). Press Save.
On Input page, tell it where Accessory 0 comes from (Type is which RC signal protocol like PPM or SBus, Number is which RC channel in that protocol) and adjust the Min and Max for that RC channel if it needs to be different than 1000/2000. (You can also consider using Start Transmitter Setup Wizard or Start Manual Calibration to help you set the correct Min and Max. Try it. It is easy.) Press Save.
I assume that 50Hz PWM is OK. On the Output page, configure Accessory0 to have 500us for Min, 1000us for Neutral (not really necessary), and 2000us for Max. (2000us at 50Hz is 100% on.) It won't let you save less than 500us in this normal setup page. We will fix that later. Press Save.
Select System tab at the bottom of the page.
Expand Settings by clicking on the arrow beside it.
Expand ActuatorSettings by clicking on the arrow beside it.
Expand ChannelMin by clicking on the arrow beside it.
Note that these are numbered starting at 0, so for output #6 you will need to set [5] here. You should already see a 500 in it.
Set it to 0.
Press the red up arrow at the top of the screen to save this permanently.
It will still show 500 on the normal Configuration Output page, but you can see the real value here on the System page.
I haven't tried this, but it seems the right way to get it working.