Annoying way I've caught myself between Ryanair and agent. I didn't want to book layover flights myself (painful using Ryanair website) so I've used one of the agent sites.
If you wanna do online checking you need to login using email and not PNR+last_name like most sites. Of course agent used their email and flight was early enough that agent wasn't reachable by phone when my flight commenced. I had to pay 6x20 euro fee at airport for printing a boarding pass, which is a dark pattern by itself.
The thing is you can't do proper layovers with budget airlines. Those third-party sites that try to make it happen are incredibly dodgy and if something goes wrong they have no legal obligation to offer proper rebooking since they are not required (and usually don't) have any sort of partnership with any of the airlines.
If I wanted to make a connection with a budget airline I would always allocate at least one night at the intermediary stop since you need to leave the duty-free area anyways, just in case something goes wrong. It's just not worth the risk.
If you wanna do online checking you need to login using email and not PNR+last_name like most sites. Of course agent used their email and flight was early enough that agent wasn't reachable by phone when my flight commenced. I had to pay 6x20 euro fee at airport for printing a boarding pass, which is a dark pattern by itself.