Did you read the article by George Huey in MSDN Magazine?
It covers transition from an existing SQL or Azure SQL DB to a DB with federations in the section called "Migrating Database Schema from SQL Server or SQL Azure to SQL Azure Federation".
Right after that I would recommend to read the tutorial on data querying (part1, part2).
You will have to change your queries if they want to access the data from federations. Basically, every federation is an independent SQL database and you have first to establish connection to correct federation before querying for data.
There are also some peculiarities how to use federations with Entity Framework, partially due to additional overhead for connection to federation instance, and partially because federations do not provide support for MARS operations (article).