First I'd like to say welcome to the flier community

. Flying is fun, and so is the adventure of getting onto and off of your flights.
I'd like to say up front this was Disney Travel's fault instead of yours or American Airlines. Disney Travel, acting as your agent, should have booked all the seats in advance and explained the process to you. Since they did not, they did you a disservice. Next time you go on a trip and would like to use a travel service (which is a great idea, BTW), I suggest a local travel agent that you can visit, ask questions, and sit with while making the decisions. Same fees and commissions for them, only you have an accountable party to contact.
Several airlines, led by American in this case, have determined that travelers are willing to pay a little extra for more desirable seats ("premium" as it were). These premium seats include seats closer to the front of the aircraft as well as aisle and window seats. Initially after releasing the flight information, airlines tend to make economy class seats of most types available for reservations by the customer. However as the day of travel approaches and the flight begins to fill, AA will designate the remaining seats that could qualify as premium into this category and begin charging extra for them. If these seats are not filled with those willing to pay extra, they go into the pool for the airport.
All airlines (except maybe Southwest) hold a block of seats from the reservation system for use by airport staff. This allows their staff flexibility at the check-in desk and gate to accommodate travelers needing specific seats (service dogs, air marshals, etc). It also allows airport staff the ability to seat parties together or move someone from the exit row that isn't qualified to perform those duties (minors, elderly, etc). Since the airline has this block of seats, those without seat assignments are able to get aboard the aircraft.
Airlines have been operating in this manor for decades, so the game is well versed. No worries on getting a seat, and the two outlier will likely sit together.
I highly recommend you arrive at the airport early!
Arriving early allows time for the check-in agent to assign you a seat and move assignments around to get your party together. In addition, it will help you navigate security, use the restroom, buy drinks/snacks before boarding, and generally ensure you do not feel rushed.
By early, I mean no later than 2 hours before flight time, and it is better for new fliers to be there 2.5-3 hours early to be sure things roll smoothly. This is especially true if it is during a busy time for air travel (major holidays, spring break, conventions, etc).
Good luck, and be sure to read the TSA and air travel threads here on the DIS. They will provide lots of info for you.