Rec # (also known as RIN), is automatically assigned by RootsMagic as people are added to the file. They cannot be changed by the user.
Ref # (or Reference Number) is completely user-defined. It can be a number, characters, combination, etc. - whatever the user wants to store there. A person can also have as many Reference #'s as the user gives them. To add a reference number, you "Add a Fact" and choose "Reference Number" from the list of available fact types.
You can set RootsMagic Tools>File Options>General to select which to display after a name.
Record Number is assigned by the system, Reference Number is added by the user.