Drupal as (powerful) relational database
You have a good start on working with the databases.  From my own experience I am loath to rely/allow Drupal to maintain any sensible data.  And since you already have a robust database it sounds like it would not be a good option for you either.

With all that said, it seems like you want to simply hook into the node/content saving that occurs in drupal.  You will then be able to connect to an external database and process and insert the data anyway you choose.

Node API Hooks - D6 has similar functions, just named differently.  There are a lot of hook points in the process.  You can even alter forms and add your own submit functions.