You should include the root note id and not just the immediate note id when replying so you can pull the whole thread. Damus and branle both do this. You don't have to but it's harder to pull long reply chains if you don't.
Discussion
There should be at least two refs when replying to a non-root note: first is root, second is immediate reply, and anything inbetween are mentioned notes. It's informal atm but works well.