First make sure you have access to the repository from the WF manager. In the credentials manager on your computer with WF manager installed, make sure you are using an account with rights to the repository.
Open the SD project in WF manager, and from the file menu select Check In. You should get a notice about creating a package in the repository.
Or, you could use the import function. Select the folder in the repository and click import. Navigate to your SD project and select the main workflow file.
That should do it.
rob