We booked Aegean plane tickets (Athens to Santorini) through their web and all we have is a printout of the reservation code. The amount already hit my credit card.
Can you print out a boarding pass from their website?
How do you select seats? Or is it first come first serve with no seat assignment?
Is it a small plane with seat rows set up 2 and 1 or is it 3 and 3 across? Thanks.

You don't get a boarding pass until you check in. Just show your confirmation email and they'll issue one to you. That's when you'd normally be given a seat assignment. If you want a specific seat try sending them an email with your reservation code and the seats you want, but understand that the flights are short and comfortable.

As far as I know all of Aegean's fleet are commuter jets with 2+2 seating, holding around 100-168 passengers, no little old puddle-jumpers like some of the outdated Olympic fleet.

Or they might be 3+3, I can't remember clearly.

yes brotherleelove2004 it's usually 3+3 (at least with the ones i've flown)!
Labern you could send them an email like brotherleelove suggested, but i doubt they will take it under consideration. But the flight really is very easy, and apart from that, you can ask for your preferred seat at check in.

Thanks, I had a nagging feeling they were 3+3.

We flew Aegean from Athens to Chania this past June and the configuation was 2+2. Very comfortable seats, very polite and helpful attendants and most importantly the plane left right on time. Have a great trip.

I just did the opposite and flew Santorini to Athens last week. The seats were 3x3 and they were comfy. Although I think my reservation info suggested the flight would be 45 minutes, I think it actually lasted about 20. I can't help you with seat assignments... I just showed up and was assigned a seat then. Good luck!