An application acts as a wrapper for all related datasets. All user-items interactions inside one application are considered related to each other by Xineoh’s algorithm.
How to decide on one or multiple applications.
In general, different websites would each have their own application because user behaviour could be different between domains. It is, however, possible to include all interactions across multiple contexts (domains as an example) into a single application and explain differences in behaviour to the algorithm through context tags. Sharing users like this is more complicated but could have advantages like improved cold start and improved accuracy from better data density.
When in doubt you should consider splitting rather than combining datasets into separate applications.