Any custom tables you add to the database will not be overwritten or dropped. Just make sure you give them a total different naming convention you can keep up with.
If you plan to use any of the API with those tables, I'd suggest using custom tables to store the data in. Only reason is it makes things easier to access and manage plus you get full functionality out of them. Plus you get the UI to manage your schema as well as the data. You can use the Kentico form controls to perform validation on your data entry and updates without writing any code.
You can create a custom table based on an existing table, which works pretty well.
You can also import the data using the import toolkit. I do believe this requires the structure of the custom table object to already be in place.