Please be careful in using commercial sites and do not buy a full price ticket. They are useful in planning but unless you are sure you are only buying a reservation/seat only ticket check with the community first.

So for clarification:

The app has 3 sections pertinent to travelling, that collectively create your free travel ticket. The only extra you may have to pay for is a reservation (normally a few euros) or in a few cases there is an administrative toll *for example travelling in the Italian section of the Brenner Pass).

Firstly you look for your options for desired journey in the PLANNER section. AS you rightly note the IR planner is not complete so you use any number of other train planning sites to seek your journey.

If you find a suitable train in the PLANNER you use the tab to add it to your PASS, which is the diary of your intended and taken individual  train trips for your PASS. If you can’t find it in the PLANNER in the app but find it elsewhere you can add the train(s) manually to your TRIP.

To travel on a train you transfer it shortly before boarding into your PASS, using the slider. Then in your PASS you simply press the SHOW TICKET button and you will see a QR code and the train details underneath the QR code.

This is your ticket to ride and you can add as many  trains in the travel day as you want. You can remove a train from your pass and replace it as many times as you want, similarly with your TRIP.

Some trains have the opportunity to get a reservation, sometimes compulsory, and these are completely separated from your pass, even if you but them from Interrail via the app or website.

There are tutorials etc through the community.

Hey,

Omio is not a national rail page, but only a commercial website. 

There is no direct nighttrain between Talinn and Prague. Between Warsow and Prague, yes.

Travelling by train in baltic states is not so good. There are almost NO trains between the countries. Only busses, but they are not part of Interrail. 

Maybe @rvdborgt or @AnnaB know more about travelling there, but I would suggest to not go there. Often there are problems with train staff that does not know what interrail is in baltic states.

Trains in the Baltic states can only be found on the operators’ websites and hardly elsewhere, because these operators don't share their timetables with the rest of the world (although Lithuanian trains sometimes do show up elsewhere). In addition, Omio is not a reliable train planner and neither is the rail planner app.

For the Baltic states, please check Seat61.com to get an idea of what's possible.

Traveling in Baltics by train is not so easy but it can be done (except Lithuania  Latvia ATM).
As already suggested consult seat61 for more information.

In Lithuania using Interrail is pretty straightforward. Just hop on the train(s) and they will give you your ticket there if you show your Interrail pass.
Only for the Vilnius-Siauliai-Klaipeda route a reservation is neccessary during high season (1st class it costs 5 euro, 2nd class free).