There are a couple of ways to do what you are asking, i.e., mapping data from two database sources to a target (let me know if this is not what you meant).
1. Define an intermediate database and have two transformations that transform from your two database sources, then another transformation from the intermediate database to the final target.
2. Define a transformation from the database source where most of the data comes from, to the final target. Then get data from the other database source using DBLookup() in the mappings.
Let me know if you want me to expand on either of these points.
A third way will be added in a future version, and that is to enable multiple sources and targets.