Please understand that BoxCryptor is an interesting and very useful system that can be used in combination with _many_ other tools and online storage providers. Because of that, it's not always possible to reply to forum posts in case forum members are unfamiliar with a particular tool, in this case SuperFlexibleFileSync.
Maybe it is of some help if I describe the way we use BoxCryptor, I don't know. Other forum members may have much better ideas, perhaps they have the time to add their comments.
o) To start with, we always separate system files and data files as much as possible, most system information and executable files are stored on C:\ and most data files are stored on D:\
We never use the default C:\ Documents, Music, Pictures, Videos location. Nowadays many desktops, laptops are configured that way, that is, a separate system and data partition.
o) BoxCryptor has the notion of a BoxCryptor Drive ( typically Z ) and a BoxCryptor Folder. The BoxCryptor Folder is the encrypted storage area of the BoxCryptor Drive and the BoxCryptor Drive is the unencrypted view of that encrypted BoxCryptor Folder:
o) We often define 1 toplevel D:\ located BoxCryptor Drive Z and a number of sub-toplevel folders in that toplevel BoxCryptor Drive.
The BoxCryptor Drive is the only way to access our data.
You can use the synchronization program you mentioned, provided by syncovery.com (formerly superflexible.com), to synchronize the toplevel BoxCryptor Folder or the sub-toplevel folders. In our approach we prefer to have synchronized encrypted copies on each of our computers and cloud storage systems (or LAN / NAS storage), we do not use 1 centralized and shared encrypted LAN or WAN storage location.
Although we use multiple online storage providers, multiple encryption mechanisms, and although not all computers we use need the same encrypted sub-toplevel folders to be synchronized, the abovementioned modest scenario is basically what is used on our desktops and laptops as far as the use of BoxCryptor is concerned.
I'm not sure whether this helps, but let us know.