Let's assume you're talking about the
amc script.
1.
You can use folders such as "Movies" or "TV Shows" to force auto-detection one way or another. See
amc script manual for details. If you wan't custom folder names, then you have to use labels. If you can't use labels, then you have to go with folder naming conventions.
2.
It's your call. filebot expects to be called on completed files, and can't check or guess if some other 3rd party process is still somehow sometimes writing to the file. Typically, in automated setups, the 3rd party software will call filebot on newly completed files, and never all filebot on in-progress files. You can also do your own logic, such as excluding and ignoring files that have been modified within the last X minutes.
3.
Your call. Either will work fine. Depending on what you're doing, and how you're doing it, how much control you have over the remote server, etc, one might work better than the other. I'd do things locally. It's easier to reason about. You have a scheduled task once day on your local machine that you control and understand. Task calls rsync to sync files, then calls filebot to organize files. Done. Neatly resolves (2) as well since filebot won't be called until rsync is done.
PS: Meet
FileBot Node ➔
viewtopic.php?t=2663