Seat reservations and the app are completely separate. They'll never appear on the app. Whenever asked show the PDF (seat reservation) and the app (pass).

You need to add any train to the app before boarding : it doesn't matter whether it requires a seat reservation or not. You can do that at any point.

On which route are you unable to travel in 1st class ? This seems weird. Only some regional trains do not offer 1st class.

It's best to avoid eurail.com to book seats, esp. for optional seat reservations : extra fees (2€ per person per train) and sometimes more expensive. Have a look here :

https://www.seat61.com/interrail-and-eurail-reservations.htm

https://community.eurail.com/train-connections-reservations-47/how-to-get-reservations-105

Do not hesitate for questions. With a 1st class pass you can get free optional seat reservations in Germany, Austria, Czechia, Hungary,... through tickets.oebb.at.

I need some more help understanding all of this.

1. When you say PDF seat reservation  & the pass- what are you referring to? I have an invoice stating that I have paid for seats which are stated as 2nd class and there no seat numbers or names stated. 
    
2. How do you add the train to the app? Which app? And why do you need to do this?
3. If I’ve paid first class then why does it assign me to second class or do we just go to first class?
4. what do you mean by “don’t book eurail.com for seats”? Why? Do seat reservations need to be linked somehow to your original eurail pass?
5. I did buy tickets from Oebb from Brussels to Berlin but it doesn’t seem to run between all countries. And it only gave me one ticket even though I wanted an adult and a youth. Are they combined on one ticket? 

First to make sure, do you have a Eurail pass ?

1. Before boarding you add to Rail Planner app any train you'd like to take. This gives you a QR-code (your ticket for the journey). On top of that sometimes seat reservations are mandatory. On those trains you need to show both the seat reservations booking (usually in a PDF form) and the pass on Rail Planner. 

2. See 1

3. It shouldn't assign you 2nd class seats if you have a 1st class pass (unless 1st class is sold out which is unlikely). What is the problematic route ?

4. It is best to avoid eurail.com to book seat reservations and to make them through the railway companies websites. More reliable and cheaper (you avoid booking fees). Seat reservations and the pass/app are completely separate, that's why you need to show both whenever a ticket inspector comes.

5. Yes, optional seat resrervations are combined on one ticket. You should see 2 seat numbers though. They are free with a 1st class pass through tickets.oebb.at.

Hope I could help a little. English isn't my mother tongue so sometimes I struggle a bit to explain