For Our KTunerECU R1 hardware the Flex Fuel runs to a pin right on our board. See Revision 1 Hardware Pinouts.
Software:
On platforms where the option needs to be enabled you'll find an enable checkbox in the Flex Fuel section. This may mention the input pin, or let you choose the input to use, depending on the platform.
Three base adjustment options are available for Flex Fuel control based on ethanol content (Ethanol %):
Fuel %: Adjusts fuel injector delivery quantity based on ethanol content. This is typically not adjusted from the default values shown.
Ign Adj: this is an over-all ignition adjustment based on ethanol content.