The recommended mode of operation is to notification emails to drive updates, either manually (you can drag story links or blocks of html/text containing story links onto the FFF plugin button or into the FFF Add Stories from URL dialog) or with FFF's email integration. FAQ:
https://github.com/JimmXinu/FanFicFa...ck-for-updates
If you choose to download a bunch to start with, I recommend only doing smallish groups of stories at a time (say 10-30) and waiting 10-30 minutes between batches.
Those are just my guesses, however. I don't have any firm data on when AO3 starts blocking or throttling users making too many downloads, but we do know it can happen.