Assuming that the first two operations create multi-record targets, then the best way to have multiple sources for the third operation is to store your results in database tables vs files. You can select from multiple tables and create a relationship between these tables in defining your source.
If you do not have a database readily available, you can use PostgreSQL provided as part of the Jitterbit Server to test this out.
The current functionality does store global variables that can be used between operations, however, the current version does not support global variable arrays. We plan to provide this. We also plan to provide support for mutiple sources (different database and files in one source).
Please tell us if you need further assistance.