For good reasons, FileMaker will only import single databases at a time (the UI for importing multiple databases with the possibility of multiple structures would be just nasty). The import folder command in FM6 is for importing data into records (one record per file), and is not what you are looking for.
What you want to do is to open the file you are going to import from, do a find so that only the records you want to pull over are selected (if you want all of them, then "show all records"). Then open the file you want things imported into, and select "Import" (from file). Then you just walk through the process of matching up the fields, and let it import the new records.... Oh... and along the way you will want to select "add new records".