Which DBMS ?
Each DBMS has different facilities available and different capabilities,
especially when it comes to linking two databases together. If you are
migrating everything, you'd probably be a lot easier putting it all into one
database which will save you have to use "federated" support to join across
You also have a chance to think whether you want to change DBMS.
Are you talking about modifying the structures ?
If so, the book "Refactoring Databases : Evolutionary Database Design" by
Scott Ambler and Pramodkumar J Sadalage (Addison-Wesley, ISBN-10: 0321293533,
ISBN-13: 978-0321293534) is a great primer for the types of changes you will
have to make.
The biggest challenge you are going to face is making modifications while not
breaking existing applications (I assume you have existing apps).
If I can be any help then drop me a line : especially if you wish to consider
DB2 as the DBMS of choice going forward. DB2 has good Rails support, and
getting better by the day, and the free DB2 Express-C has no limit on
database size, only on memory (4 gig) and processors (2 sockets, not cores).