I can't say I've ever tried it but I don't see why you couldn't set up a separate Data Mart database per instance and enable both of them within the Configuration Console. You should be able to see all the GP databases you've enabled within MR then. When you set up the Datamart database you specify which GP server (and instance if not using the default). Then when you click on the integrations in the Configuration Console you can enable the appropriate databases for each one. Once it’s fully integrated you should see the different databases in the Report Designer.
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