You can have both at the same time: Copy DK_System of DK-Lite to your Kindle and approve when it asks for replacing files and merging folders. And copy appropriate update file. then use update feature of Kindle.
I think I ve read in Duokan forums that you dont need to copy any update file to install lite over Duokan, you just need to copy the DK folder. And at least in my case it worked fine!