Hard to say exactly what you would need but it sounds like you could consider either BULK INSERT or SSIS to get the data from file to the database. Then you would execute your insert / update depending on what you would want to do. This is typically done using "staging" tables where you would load data from files, scrub, and then finally execute any other processing that you would need to do against that data.

Hope this helps. If you provide some additional information we might be able to provide you with further details Regardless, looking into BULK INSERT should get you on your way.