The import tool does give you options about what to do when there are duplicate items - overwrite the destination with the source or keep the destination. In order for this to work correctly, you need to select the option to use the internal ID instead of the name to determine duplicates.
Also, in order to import instances you need to check the box next to something like "Include Instances" (I'm not sure of the exact wording) that appears belows the folder and object list when you're selecting files to import. If you have a LOT of reports or instances (from experience, over 1,000), you may want to import in sets instead of trying to import the whole thing. Depending on the version of BO XI, the Import Wizard is more likely to have errors when you try to import large numbers of objects - especially if you use .biar files instead of importing from one system directly to another.
-Dell
A computer only does what you actually told it to do - not what you thought you told it to do.