Flying hooks in Pro Tools or any other DAW has never been easier. When I first started as a engineer that was not the case. I would have to record the full hook then mix it. After that I would sample it into a sampler like a MPC. The final step would be rewinding the tape and waiting for the next hook to come and as soon as it came I would hit the sampler and pray that I got it on time. Sometimes I would have to do this ten to twenty times before I got it right.
Anyway times have changed, and below is a video on how I fly hooks.