In the projects when the advanced fluid simulation is required (ex: Chocolate, milk splashes etc.), we are using real flow but when we need to achieve more complex animation, we finish it in Maya and send it to 3ds Max.
As for the render engine, we have decided that this is a great project to use FStorm because there is not much subsurface rendering and therefore due to the GPU side of FStorm the render frame was only a few minutes. For that reason we are looking to turn to GPU renders whenever we can. In case that the project requires something more complex, we use the CPU render engine.
Our biggest challenge in this project was adapting our existing pipeline to the Fstorm render engine. When you change something big such as the type of render engine, you have a lot of R&D work to do in order to learn how this tool/software works and to implement it to the existing pipeline.