You can do it both ways like you've mentioned above. If you leave FUA=0, you may end up with the issue again. But you can "assist" the auto-leaning by manually entering a value and it'll auto-learn from you.
'14 S5 DSG
'09 E90 M3 DCT (sold)
[Evolve ECU/TCU|MS Pullies|K&N drop-in|Test Pipes]