You can exclude directories from synchronization by using the Dropbox CLI. You add directories to the exclusion list to disable synching and you remove them from the list to re-enable synching.
$ dropbox exclude add [DIRECTORY]
Partitions that are mounted at system startup are configured by including them in `/etc/fstab` as shown below. Here's a more detailed explanation that should get you going.
#
/dev/sda2 /home ext4 defaults 0 2
Finally, If content is deleted from a synchronized directory the deletion will reflect in Dropbox. However, Dropbox has a versioning system that can be used to undelete content as well as undo changes.