Returning to the Stagg airships, once you have unlocked them in the main storyline, is not difficult. You can make it over to the Alpha airship after you glide towards it, off the rooftop of one of the tallest buildings on the Founders' Island. You need to land on the airship and find the manhole shown in the above screenshot, thanks to which you get to the foyer.
It is even easier to get on board the Beta airship. After you have made it onto one of the tallest cranes around, you only need to glide towards the destroyed front part of the airship shown in the above screenshot.