I just went through this myself last year as I was planning my honeymoon. It was my first trip to WDW as an adult, so it was my first time planning it. For me, planning the trip was 1/2 the fun. I loved going on the WDW website, checking out all of my resort options, configuring different packages, looking for the best airline rates on Expedia.com and other travel website, and just generally planning the trip.
I'll give you my real quick answer, and then I'll expand on it later. (You can just skip over my long winded response if you like. I won't be offended.) I would book resort, then flight, then ADR's for 2-3 meals during your trip (I was able to wing it most of my honeymoon), and above all, plan on using Disney transportation as much as possible. The Magical Express from and to the Orlando airport is wonderful. And you can walk, take a bus, boat or monorail to anywhere on Disney property that you would want to go. It is a huge money saver when you don't have to rent a car or worry about a taxi.
Ok, so that was my short answer. Here is the directors cut, extended version of that. The first thing I did (if you haven't already done so) is figure out a budget. I set a limit on how much I could spend on what I call "the four horsemen of travel" -- airfare, a vehicle at your destination, accommodations, and food. I first got a general idea of how much the flight would cost me. I had read all about the different free travel options from the airport and on Disney property, so I knew my budget for Disney property transportation would be $0.00. I went to AllEarsNet.com and checked out all of the menus on that site. This gave me a good idea of how much we'd be spending on food while down there. (As it turned out, after I had my resort booked they introduced the free dining plan, which I was able to add on so I was able to have more money for souvenirs.) This exercise gave me a ballpark figure of how much I could spend on resort accommodations.
I had already made up my mind that I would be staying onsite, so after I had an idea in mind of how much I could spend, I had to figure out where to stay. This is one of the more difficult parts of the planning. Each resort level and each individual resort in that level have their own plusses and minuses. So try to figure out what you want out of your resort, and find one in your budget that meets your needs. I started by configuring different packages online at different level resorts. After about a week of doing this for 30-45 minutes every night, I was sold on a resort (the Contemporary) and a room level (Tower). I already knew that I would want park hopper tickets for my entire stay (minus get-away day since we wouldn't have any time to hit a park before we had to leave for the airport), so I had already included that in my package.
After I had this all figured out, I called Disney directly to book my package. I had the printout from the website in front of me, so I told the CM exactly what I wanted. After a 10-minute phone call, I was booked at Disney World!
The next step was to keep an eye on airline rates. When they got to a point where I didn't think they would go lower, I booked them as well. As it turns out, two days after I booked my flight the rates went up about $50/flight. So I was happy.
Then I started on our meals. We printed off a few menus from AllEars that looked appealing to us. We then decided where we wanted to eat, and what days we wanted to eat there. And at 180 days out, I called and made my ADR's. The last step in this process was the most difficult -- the waiting!!!
Well, if you made it through this far, I hope I was able to help you out a little bit. Happy planning!