The answer depends on how the tune in the ECM is set up.  Most aftermarket ECU's can be configured for almost any alignment of the cam sensor.  The Vendor/Tuner/Support people should be able to tell you.
However,  it seems likely that any "base tune file" would have been developed on a "stock configured" car,  so 25 ATDC #1 (falling edge) is likely the right place to start  
Bob