After setting the exact scale length by adjusting the distance between all bridge saddles and the nut at 648 mm (25,5″), if you have Fender, Ibanez, Schecter etc. Do the same procedure if you tune a guitar with Gibson scale: 628 mm (24,75″).   You do it In exactly the same way you would intonate with a standard neck – by matching the Thidell Formula 1 open string notes to the octave (12th fret) notes.