Good practices working with databases
Your entity-relationship model is likely going to map to what we call 'Content types' in Drupal.

Content types are defined using the Content Construction Kit module, commonly referred to as CCK.

With CCK, you point-and-click to define what fields you want the content type to have - text fields, numbers, links, references to other content types, references to users in your Drupal site.

With the content types defined, you can figure out what kind of lists for that content you want - tabular, blog-style, etc, and use the Views module to create that listing.  Views is a point-and-click query builder, complete with sorting, filtering, access control, dynamic URL arguments, and relationships (think joins) to other content types.

That's typically how 'databases' are done in Drupal - but you don't have to do anything with the database at all, really.

If you've got a really specific use case that can't be solved with some combination of the 7000 or so contributed Drupal modules, then it might be time to grab a copy of 'Pro Drupal Development' and learn module development to integrate your custom module into the rest of Drupal to meet your exact need.