For organisations that are using migFx on one programme with a number of projects or a Supplier that has a set of standard operating procedures it makes sense to set up the Item Manager at the Portal level so that all the Projects use a standard set of Item Types all configured in the same way. 

But if a single implementation of migFx is being used to manage projects from a number of organisations that wish to use their own procedures or terminology then the settings can be managed at the individual Project level.  in this way the differences between organisations can be accommodated but they can all use the common environment without having to install migFx multiple times.