While yes you can use Magical Express regardless of which airline you use, there's also something available at WDW called Resort Airline Checkin which allows you to check your bags in to your airline right at your WDW resort. This is only available for people flying on participating airlines. Currently, the following airlines are listed as participating: American Airlines, Continental, Delta, jetBlue, United, Alaska Airlines, AirTran, US Airways and Southwest. Disney will pick your bags up at the airport and deliver them to you at your resort (as long as you land before 10pm) regardless of your airline but you can only use RAC if you fly one of these airlines. If you fly another airline then you have to stow your bags under the bus for your bus ride to the airport and then check your bags at the airport.
The majority of the time, you will not get a better price booking airfare through Disney. Disney also only deals with a couple airlines. Book your airfare yourself. Youll just need to let Disney (or your
travel agent if you use one) know your flight information to register for Magical Express. I like to look at sites like kayak.com to find the best prices and then go directly to the airlines own sites to book since its usually slightly cheaper on the airlines sites. I also check southwest because they wont post on sites like kayak. Remember when comparing fares that you really need to include all the fees (seat assignment, luggage) in order to get even comparisons.
Flight times really are a matter of preference. Im fond of early morning flights for our outbound flight because my family is early birds anyway plus theres less chance of delays. The later your flight, the more likely you are to encounter delays. I think more people prefer later morning flights heading out. That being said, I like late flights coming home. In my case Ive got a much shorter flight than you do and Im in the same time zone as Orlando. Youll be crossing 3 times zones and have over a 7 hour flight. When we flew a family member of ours out to Orlando from LAX we chose a flight out of LAX that would hopefully beat the rush hour traffic (they used a shuttle to avoid traffic anyway) and then flew them back out so that theyd land late afternoon in LAX so theyd get home in time to throw on some laundry, get some sleep that night and still be able to get to work the next day. Its very much personal preference.
Normally I like nonstop flights because one of my kids gets a lot of ear pain going up and down, but for a long flight like yours Id likely choose a flight with a stop so we could all stretch our legs. Its really hard sitting in those small seats for a solid 7 hours, only getting up for bathroom breaks. Then again, some people will take the nonstop every time because there are less chances of problems without connections and nonstop is simply faster. Again, its personal preference.
Heres something you didnt ask about. Youre travelling with 3 kids. Airlines do nothing to ensure parents sit with kids other than give parents the opportunity to pay for seat assignments just like everybody else. Lots of people are not aware of this so I want to make sure you are. People who have paid for their seat assignments generally dont want to then give up their chosen seats so that a parent can sit with their child after not purchasing the seats assignments that could have ensure this. Please purchase the seat assignments for your family if you want to be sure to sit together. Also, make sure to check your itinerary weekly to be sure that you still have your seat assignments. If the airline makes some kind of change to the itinerary or equipment, seat assignments can disappear. Its very easy to call the airline and have them re-instated but you do need to call. Its very frustrating to people but it just is what it is. The only airline where this isnt an issue is Southwest who doesnt do seat assignments. They do open seating where you board the plane and choose your seat. Boarding is based on boarding positions. After people who pay full price and business class, they then assign boarding positions to those who pay for Early Bird Check In and then just assign the rest as people check in (you can start checking in a 24 hours before the flight. I would recommend paying for EBCI since youre an inexperience flyer. Most likely youll get A boarding passes which means youll board in the first 1/3 of passengers. If you do get a B boarding pass (second 1/3 of passengers) then you can always take advantage of family boarding between A and B, at least for one adult and your 2 year old. The short version of this long paragraph is that I really, really, really recommend paying for whatever option the airline gives to ensure seating together.
Have a great trip!!