Here is what I would do, if you want to go on submarine excursion.
BOOK IT YOURSELF!!!
We saved money by booking it ourselves, and we got a noon reservation also. We didn't need to rush off the ship like everyone else. We also picked up 10% off coupons in the Tourism office (make sure you grab a coupon book for each person) One coupon is not good for all - everyone must have one.
Disney charges more for a child ticket than Atlantis does, so we save over $35, plus 10%.
I also talked with the people from our cruise that got off the sub just before we were going and they said it was PACKED like sardines. I believe the sub holds 45, and they said they had to share windows. When we got on, there were only about 12 of us. We were able to move around, and switch back and forth and from side to side to view. For those claustrophobic people definately book it yourself. We went last year on the Halloween cruise, this may be off season, but Atlantis says that the noon tour always has less people.
HAVE FUN! My son and daughter were 3 and 5 at the time and we saw lots of little sharks, a turtle, a few sting rays, and a lobster.