If you plan to use your Roma Pass at the Colosseum and Borghese, but go to the National Museum before the Borghese, then DON'T show your Roma Pass at the National Museum. You won't get the discount, but you have to use the 2 free entries first--there is no way to pick and choose.
If you use the Roma Pass for your Colosseum and National Museum entry, you will have to purchase tickets for the Borghese separately. Whether you can reserve and then pay for the tickets (getting the slight discount) later, I'm not sure.
As the other poster noted, the National Museum is cheaper, so most people prefer to use their free entry at the Colosseum and Borghese.
If you do decide to use the Roma Pass free entry at the Borghese, you must still reserve and you cannot do it online. They will give you a confirmation number, and that plus the Roma Pass (that still has one valid free entry) is sufficient.