When you have installed BoxCryptor, you have defined
(1) a BoxCryptor Folder ( the location of encrypted user files / directories ).
(2) a BoxCryptor Drive ( default "Z" )
These definitions can be seen when you right-click BoxCryptor's icon in the system tray ( bottom-right of your Windows desktop ) and then select BoxCryptor's Preferences.
Each time you create an unencrypted user file / directory in the BoxCryptor Drive Z, BoxCryptor will create the corresponding encrypted user file / directory in the BoxCryptor Folder.
The BoxCryptor Folder mentioned in (1) will always be the encrypted view of the BoxCryptor Drive mentioned in (2).
The BoxCryptor Drive mentioned in (2) will always be the unencrypted view of the BoxCryptor Folder mentioned in (1).
The encrypted BoxCryptor Folder is actually the (encrypted) storage space of the BoxCryptor Drive Z.
Put your files / directories always in the BoxCryptor Drive.
Get your files / directories always from the BoxCryptor Drive.
Never put / create your user files and directories directly in the BoxCryptor Folder (1), the encrypted folder, BoxCryptor will do that.
Never upload your files from the BoxCryptor Drive, the unencrypted Z drive, the unencrypted view of your files / directories, to an online storage system like GDrive, because in that case you will upload your unencrypted files to GDrive.
In other words, again, the BoxCryptor Drive Z acts as a sort of filter, everything you store in it, is actually stored encrypted in the BoxCryptor Folder.
Everything you retrieve from BoxCryptor Drive is actually retrieved from BoxCryptor Folder, but can now be viewed / accessed unencrypted.
The only case where you use the encrypted BoxCryptor Folder mentioned in (1) is when using for example Google's Drive. You point the Google Drive to the _encrypted_ BoxCryptor Folder, never to the _unencrypted_ view as provided by the BoxCryptor Drive.
This way, all your files will be stored encrypted in GDrive.
Hope this has made it more clear, not more complicated ;-)