Usually a WEB Application stores a file based database like MS-Access in its APP_DATA folder under the root of the site where every permission is granted to the IIS Service.
Then in your connection string you refer to this location using
Connection = @"Provider=Microsoft.ACE.OLEDB.12.0;
Data Source=|DataDirectory|\Waypoints.accdb";
On the server side there is no need to install anything apart from the Microsoft Database Access Engine appropriate for the bitness of your web application. (32bit or 64bit)