Normally a Power BI Desktop file (PBIX) contains your queries, data model, and reports (visualization). Looking at a multi-file strategy, we split this up into two (or more) files.
The first file only contains the queries and data model. The second file is directly connected to the first one (direct query) and reads the data model. The file it selves includes all report content like visualizations, booksmarks and everything related to that. By working this way, you will be able to build multiple reports based on the same dataset.
Click through for a demonstration.