Mursit, welcome to the forums! If you move this over to the Server Admin section of the forums, you're more likely to get an answer.
good question. The way that we've gone about this is by naming standard. We've appended _M onto the end of the datasource that lives on our Marketer site. And typically we do not publish datasources directly to here, but rather we use a script that looks for changes on the default site and then adds appropriately onto the Marketer site.
One thing to consider is that data sources are site specific. That means that when you are logged into the server, you should only see the data sources that belongs to the site you are on. In Tableau Desktop, you are asked to choose a site when you login - this should help the end user know which data source they are connected.