You are free to choose the best way for you - below are two of the most common options to help you decide.
Option 1: Use a single Model/file.
This allows you to better model any interdependencies between the projects. Also, to create views of the Map at the program level. This can be helpful to engage at senior levels to show a joined-up benefit-led program whilst still having simpler project and stakeholder level views.
Option 2: Use separate Models, each is a separate file.
This allows you to separate out the projects and is helpful when each is large and complex. There may be the situation where the different projects also require different approaches as politically they need to be treated separately, or information from one can be confidential. These are examples of when to use separate models for a single program.
Our experience is that Option 1 is the most common and approach. It is also easier to start off using a single model and to split it later if needed. Option 1, therefore, gives more flexibility to change approach later.