Normally JetBlue are happy to sort out seats over Twitter if you ask nicely.
Its an international flight so go to in person check in at JetBlue and they should be able to check you in on both flights, be sure any luggage checked in is tagged to 'DUB'
If they can't issue the boarding card, when you get to BOS speak to the Aer Lingus gate agent, you have to do this anyway as they have to check your passport/visa information as Jet Blue won't do this.
On the way back, Aer Lingus, check in again in person and ask for the JetBlue boarding card and that should be issued, it helps if you have a seat allocated, but sometimes it works automatically, If they can't issue the boarding card, again on arrival in BOS find the gate agent or any customer service from JetBlue and they will sort it there and then.