You have a few options, but in short, you'd have to write a custom module for that. I've done this before for CSV and works great.
Another option is to use the Kentico Import Toolkit if you have the Ultimate license. This gives you a user interface to perform the import but requires the user to know some advanced things (connection string, table names, etc.). This would be something an administrator would do though.
Another option would be to create a scheduled task to pick up the csv or simply query a database and perform the insert/update to the custom table. I've done this as well and seems to work the best because it doesn't require any user intervention.