I do not think you can have separate installations of Eudora. Since it would make use of the registry.
As for using multiple email servers, I do not see why you cant, I have used 3 different smtp/pop3 accounts setup, one from my local e-mail server, 1 from yahoo and one for hotpop.
The data is stored under where ever you told it to place the date. Which could be in the Eudora folder, or under your login accounts profile or someplace else.
The configuration ini files would be in the Eudora folder, in the filename eudora.ini