If I use my 48 hour Roma Pass for free entry into the Colosseum can I then use it for a discount at the Borghese Gallery and if so do I need to call to make a reservation for a time at the Borghese Gallery?
Yes. Everyone is required to have a reservation unless they've purchased a tour which includes pre-booked tickets for a specific time.
not only that but you cannot use the on-line reservation facility for the Galleria Borghese. Reservations can only be made for Roam Pass visits by telephone. You need to get on it too because when they are gone they are gone.