If the destination library is on a different site, you need to use the Copy to Sharepoint action instead of the Copy item action.
Copy to Sharepoint only works on a current item that the workflow is running on, so it can’t be called directly from a site workflow. To get around this, in your site workflow you can start a list workflow on the item to be copied, and let that list workflow copy the item to the destination library. You can use a Web service query in the site workflow to start the list workflow.
For the Web service query, you need to enter a URL where the server can find the web service, this will typically be the site with the library from which to depart, followed by /_vti_bin/NintexWorkflow/Workflow.asmx
For Webmethod you select the StartWorkflowOnListItem method (click Renew after entering the URL to enable the dropdown). For itemId you use the ID you are matching with, listName is just the name of the document Library where the file is found, and workflowName is the name of the list workflow that has the Copy to Sharepoint action.
That list workflow should be attached to the document library from which the file departs, and it can just have the Copy to Sharepoint action and nothing else (or maybe a build string to build the destination url, the url should direct to the destination library), disable manual or automatic starts so it only starts through the webservice query.
To summarize, you put the Webservice query in your Site workflow, within the For Each action group. The webservice calls the list workflow on the library, and that list workflow will copy your item to the destination library.
Make sure that the account credentials you use for the Web Service query have writing permissions on the destination library as well, otherwise Nintex won’t be able to copy the file and the workflow will error.