Wow it all sounds a bit complicated, but I can help on one point, IF all your flights are with Ryanair. Ryanair is a point-to-point airline, and even if you book what looks like a return ticket (out and return on the same route) the airline considers each flight as a single contract, and so there is no problem if you just use one leg of a journey - be it outward or inward. Once the flight you booked has departed without you, your ticket for that flight is completely invalid, but that one only! If it is combined with a ticket for a flight which would serve as your return, that flight reservation is still valid as booked.

As regards the online check in, that's for you to decide - remember that you must only have handbaggage and an EU passport to use the online check in facility. But make sure you observe the online check in deadline because if you miss it, you will have to check in at the airport and that will cost you!! (You'll have to go to pay the excess fee at a separate desk before they'll complete your check in!!!)