What do you mean with “How do I get my whole itinerary for the entire trip?”

In Italy you can show the train staff only a code as reservation + eurail pass, if you mean how you can show the reservation.

When i search trips from Catania to Napoli the train begins in Catania because that is where I begin. When I look at my itinerary for the trip though it begins in Messina because I had to purchase reservations for parts of the trip. When i look at my itinerary for my trip which I was booking on the website, there is nothing about Catania. Because it is not there it makes me feel that i do not have any security for my timeline and that train scheduling could become easily mixed. Possibly i will miss trains if i am in the wrong cities because my itinerary is missing key destinations and train departure times. 

You have a reservation for the Intercity train from Messina to Napoli. You have only purchase the reservation you always need also the Eurail pass (paper or mobile version) with you and you have to write the trains that you use on the Eurail (paper) pass or choose it on the app (mobile pass).

So you take an Regionale Veloce or Regionale from Catania to Messina (you have to write/choose this train on the paper pass/app) and than probably with an Intercity from Messina to Napoli (here you need the reservation + you have to write/add this train it to the Eurail pass). You show then the train conductor the eurail pass and the reservation. 

On the Regionale (R or REG) and Regionale veloce (RV or RGV) you don’t need a reservation but only your eurail pass + you have to write the train on the paper pass or add this trip to your mobile pass in the Railplanner App.