I would go with a dynamic data website, one can easly get an interface to manage a few database tables up and running.
… that would leave the parsing of the file to do.
The down side is that it could be to complex for you to change if you don’t have much experience with .Net.
Explore Table Adapters concept in .net , The benefit of using table adapters is that you don’t need to write code for opening or closing connection programmatically. It will open and close the connection when it is required.
Second It will allow you to write query by both ways either visually or by writing it to your self. You can make your stored procedures through wizard.