Can one do incremental backups from a server with Filezilla and if so how?
I dont think you can do it with filezilla.
You could look at rsync if you just want to copy over the files that are new/changed. It is on all the linux distros, and I think there is also a couple windows ports.
If you are using windows, I am not sure if the rsync client can run in server mode to receive the files. If you are using linux, then you are all set.