The framework we're planning is divided into multiple modules responsible for single units of work and they shouldn't know about each other.
However, each module could have it's own domain objects (I know the castle documentation prefers one assembly).
I've know that you can add assemblies after Initialize by using:
ActiveRecordStarter.RegisterAssemblies(typeof(SomeModuleSpecificClass).Assembly);
However I would like each module to register itself if required and only much later actually initialize castle.
At the moment it's not quite as simple as strarting ActiveRecord first.