I am running time machine on my QNAP TS-109 for some time now. I had a few problems with the AFP share not being accessible after a while for which i found a good solution (see other post).
Enabling time machine to use (non TimeCapsule) network drives is a piece of cake. Just enter this command in a Terminal session “defaults write com.apple.systempreferences TMShowUnsupportedNetworkVolumes 1”. Once done, you can pick any share you created on your drive to use for time machine backups.
Works really well, put down here so i keep note of it 😉