Welcome aboard, Amanda! I'm happy to hear that your family will get to experience one of Disney's magical cruises in Europe this summer. I experienced a summer trip to the Mediterranean with Disney Cruise Line and can tell you from first hand experience that you are about to set sail on the trip of a lifetime!
If you'd like to try to get the main dining time, I'd suggest checking back a few times before you set sail. Quite often, guests will change their minds about their dining times, and you may find that you're able to switch to main dining at some point before you board the ship.
If you do have the second seating, however, there are some great benefits to this. My family enjoys heading off the ship on Port Adventures each day. We like to have second seating so that once we get back from exploring the ports, we can put the kids down for a nice nap, then take our time getting ready for dinner. We feel much more rested and refreshed after relaxing in the stateroom in the late afternoon while other guests are at the main dining seating. If you're worried about your little one getting hungry before that late dining time, don't fret! You can stop by one of the quick service dining spots near the pools or even order from the complimentary room service menu so you can all enjoy a snack.
Finally, you might consider booking some time for your little cruiser in It's A Small World Nursery. Perhaps you'll get to enjoy a few adults only dinners (be sure to check out Palo) while your little sailor plays, snacks and then falls asleep in the nursery after a fun day.
Also, check out the first of a
series of videos from Disney Cruise Line about the Mediterranean sailings. This will give you a nice glimpse into all the magic in store for your family this summer. Let me know if I can help with anything else before you set sail!