-trying to bring in UML to get better handle on this monster (blame previous architects, not me!)
Hehe, never heard something similar, no, that never happens, this is an absolutely rare case, yadda yadda....

Just kidding, such is life. You are not alone here. A whole lot of projects have started before UML became known practice and even today I see a lot of projects be started without a modelling base.
Usually they start small ("Hey, why do that sort of overhead for a small project") and suddenly they evolve and become large, undocumented projects.
Once we have enough stuff documented, I'll flip the development process upside down (UML first, code second--instead of re-engineer UML from existing code)
Welcome to the club- just to say that our projects are even larger and the problems remain the same.
Questions:
Well, you can have several project files of course- however I do not see the reason for doing this. One of the bigger drawbacks is that cross documentation will become a PITA if referenced parts are spread across the files.
My proposal: A system wide database repository covering all aspects of the system filled by versioned packages from version control.
The database repository is fast enough to give you quick access on all aspects of the system and allows a system wide view for modelling and documenting while version control helps restricting checkout access to parts of the model for developers.
EA supports you structuring your project with wizards, so you have a basic setup of domain/class model and GUI model (eg. Forms), however you will have to find your own way to structure the hole thing.
So hopefully that helps you further.
Regards,
Oliver