This is a good question. There is no out-of-the-box feature to do that today. But we are thinking about it.
Actually, it works in a simple case since v2.0.0: when you have your data preparation in a script of an Analysis (called "Analyse"), deploying the model will also reproduce the script (ie. all the processors).
If you have more a complex flow (with Python recipes, etc.), there is a solution: you can stack your two sources in a single dataset, then apply your flow of transformation, then split in two before modelling.
Jeremy, Product Manager at Dataiku