After a long time on the phone with Apple and trial and error, I figured out the issue. I think the problem is that they do not explain well what the purpose of Passbook is. I assumed I was going to place the APP into Passbook and access from there. In fact, the purpose of Passbook is to store your cards like a wallet (e.g. Target gift card, Starbucks card, etc) and your boarding passes. If you are flying, your boarding pass is not available till you check in, normally one day before a flight. So, you can't access said boarding pass to enter into Passbook, until you check in online. I'm going to make a suggestion to Apple that they change this, so we can access our upcoming itineraries, would be a lot easier!
But, for Amtrak, if you book a trip, you have your boarding pass on your app immediately, so, in this case, you can go into the Amtrak app, click on your upcoming reservation, and keep clicking until you get to the screen with the ability to forward your ticket, and then you will have the option to add your ticket to Passbook.
For Starbucks, you go into the Starbucks app, pull up whatever card you want to add, hit "Manage" and then you will see the option to add the card to your Passbook.
Hope that makes sense!?