Roundtrip Narita Express – different stations

I believe I have read you can do the r/t ticket for N’ex with different stations. We will start our trip in Shibuya and end it at Tokyo Station before flying out of Narita 13 days later. Any issues arriving to Shibuya and departing from Tokyo Station with a roundtrip ticket?

Can anyone explain how the roundtrip ticket works? When and how do I select the specific return train and seats? I have failed to find a YouTube video that shows that scenario.