You can upload the PAR file behind a PAR Project to the backend Software Repository directly from Eclipse. To add the PAR file to the backend:

Once the Remote Manager backend server is present in the list, you can easily upload an application from the workspace to it - right-click the PAR Project node or its provisioning.xml, and select the Install to > <RM_server> option.
In the Software Repository of the Remote Manager server, the PAR file will be represented as a bundle group built of the bundles added to the PAR Project in Eclipse and as a service application based on the bundle group.