Overwrite or skip existing files

I want to make sure that the folders on my local drive match the ones on the remote server, but if I try to upload and sync, each file is uploaded individually again (even if it already exists remotely). This is a problem because I'm looking at a 17GB upload if it does that versus just uploading those files that aren't already on the remote server or have been modified.

How do I ensure that only those files tht have been modoified or aren't already stored remotely are uploaded?

Install the latest version from here:

Then select "Synchronize" from the file exist dialog and check the [x] do this for all conflicts option.