So, quick rundown on eos:
There are two datasources: game data (eve.db) and user data (saveddata.db). Tables for these databases are defined in eos.db.(gamedata/saveddata). Most of the tables also have a class mapped to them that handles the business logic of the entity. For game data, they all reside in eos.gamedata - most of them are skeleton objects, since most eve data is simply there to provide lookup of values and not necessarily do anything. The interesting objects here are Item and Effect.
The tables for the user's data are mapped to classes defined in eos.saveddata, and this is the majority of where the logic for the calculation engine lies, and many helper functions. For example, the Module class contains logic on what a module should do (for example, it has a method isValidCharge which checks to see if a passed in Charge object is valid for the module).
A quick how to stand up a bare bones Rifter fit with an Afterburner and a 200mm Autocannon with EMP S: