There's a button in-game that's supposed to open a browser window that lets you make a DesktopDungeons.net account from your Steam account, but this didn't seem to do anything in Linux.
When I tried it in OS X, it did work. And then I could enter my DesktopDungeons.net account information on Linux and it logs in and syncs just fine.
Distributor: Steam
OS: Ubuntu 15.10