Till 1.6 Dokan was a theme only. But we changed the theme to a plugin now. So now the old system is divided into two, plugin and theme.
Dokan 2.0 is only a WooCommerce compatible theme. Nothing much.
And Dokan 1.1 is a plugin.
If you are replacing your old version or upgrading your system with the latest WooCoomerce, you just have to delete the old theme (1.6) and install the latest theme (2.0) and install Dokan plugin (1.2)