There wouldn't be anything different in terms of the configuration. The Web Part Management Utility is used to add/deploy both web part solutions to your SharePoint web application and then just make sure to run the "update master pages" command each time you add a new subsite. As for the actual web part configuration, it's the same for both where you specify the Web Access URL, Laserfiche Server, and Repository names.
Can you test by creating a new SharePoint web application (which uses a different port) and then create a single subsite for the search web part? Then add/deploy the solutions, modify the web.config file, and update the master pages and finally, try adding just the search web part there.
If further assistance is still required, opening a support case would be the next step.