Is there a reason you cannot just use the database that you import?
Are you importing the completed database or just changes?
What type of DB do you want to setup? DB2, SQL, …
Once you have answered those questions, and you decide you want to create a relation DB; just design it however you want to use it. It makes no difference because if your input does not change, you will need to run a conversion program every time you receive a new file.
Read a record from the Access file and then write/update records in your DB.