If you use odrive, first let it sync all the folder structure and than start the sync itself. I’ve used this command to sync my media folder:
exec 6>&1;num_procs=10;output="go"; while [ "$output" ]; do output=$(find "$HOME/odrive-agent-mount/Amazon Cloud Drive/Media/" -name "*.cloud*" -print0 | xargs -0 -n 1 -P $num_procs "$HOME/.odrive-agent/bin/odrive.py" sync | tee /dev/fd/6); done
If you change "$HOME/odrive-agent-mount/Amazon Cloud Drive/Media/" to "$HOME/odrive-agent-mount/Amazon Cloud Drive/Media/Movies" for example it will sync the Media --> Movies folder from amazon. The other folders would still have the folder structure though, but files are not downloaded.