I am flying EWR-LAX-SFO-EWR on DL next week. When i went to book online, I saw that it didnt let me enter my onepass number, so I just called and made the reservation over the phone. You will be fine if you give your ff number to the gate agent when you check in. If you are still concerned, just call the delta reservations number and tell them you want to credit your miles to your onepass account.