Hi @nsanz,
Version 1.4 allows top-level folders to be in different locations. 
You can explore this feature by going to your Insync app window. Click on your account and right-click any top-level folder. You’ll see change location. If you click that, a pop-up window will let you choose the top-level folder’s new location.
Please take note that this cannot be done yet for subfolders. Thank you!