Hi Simon, 

The data collected will be on the fact sheet of that object. Meaning if you describe attributes of an application, that data has to be collected on the Application fact sheet. If you describe attributes of an organization (e.g. where they are located, what type of business unit, etc.), that data has to be collected on the Organization fact sheet. 

Then, if you want to describe the relations between Application and Organization, that data will be made visible on both fact sheets (unless you restrict it). This way, one can look at the Organization and view related Applications, when another can look at the Application and see all related Organizations. With configuration you may expand the data collected on the relation to provide some other context if you need (example: Functional fit of an application may differ from one Organization to another)

There are best practices in the section Fact Sheet Modeling guidelines of the documentation https://docs-eam.leanix.net/docs/modeling-guidelines 

Hope it helps, 

To expand on Fab’s response, you can enter the relationship starting from either fact sheet. No matter where you enter it, the relationship will look the same. It really is a process decision within your org, and frankly you don’t need to define where it will be entered as it doesn’t need to consistent where they are entered.