The master file will usually be considered the file at the bottom and the overlay that goes on top. The app offers the ability to place them either way. In most cases, the app will combine multiple files with each other.
The app offers different strategies for this, explained in the documentation. The app combines multiple master files with multiple overlay files. The files are merged before they are combined, and the result will be a single PDF.
The introduction of Overlay PDF has greatly improved the existing workflows through Switch Server. Fantastic addition!