That's how it works
I've just setup similar myself as a test, I'd guess of the three sync settings you'd want to use 'Contribute' so deletions aren't replicated across.

You will need to setup a schedule to run it but that's detailed quite well in the help menu.

Edit: That's assuming you want to use it as a backup against accidental deletions, If you just want to protect against drive failure then the default sync will delete from D: when you delete from C:
(bill, Wed 14 Oct 2009, 23:15, Reply)