Flights, it depends I know people have found good prices close to their holiday but I personally prefer to have them booked if I am booking other stuff in advance.
I have been to Fl twice and never visited Disney. Just did not see it was worth the money just for a few thrill rides. I want big thrills and not to bothered about all the details.
So you could decide to do one lot of parks or the other, it will save you a decent amount of cash. Most of the parks discount multi day passes with I think 2 week passes being about the best value. So if you are only going for 2 weeks its pointless getting 2 weeks of Universal/seaworld and 2 weeks of Disney.
There are plenty of places that sell tickets. But watch out for the dodgy ones.
http://www.orlando-ticket-deals.co.uk/
We got ours from here and it worked out cheapest for us to get Universal 2 park ticket, Discovery cove ultimate ticket that then covered the rest of the parks as we wanted to do DC anyway.
I would really recommend Discovery cove, its an amazing day and a beautiful and relaxing place to be. It looks expensive but if you work it out with tickets to Seaworld and Busch its not that expensive for an all inclusive day out.
I found a good place to find info was on the trip advisor Orlando page. But there used to be a few Disney drama queens over there so it got rather annoying.
I have stayed in a hotel just off idrive which at the time was a Marriott and it was very nice. There was a daily bus transfer to Universal (after opening time) and there was one back in the afternoon and one in the evening. But Taxis were so cheap from there, all under $10 no matter how slow they drove
Seaworld was easy to get to on the buses. I would recommend Lynx buses rather than the I trolley. Lynxs goes a lot further and you can get to Disney using them if you want. I trolley just goes more or less up and down Idrive and has rubbish air con and is normally packed with tourists. On lynx they have good aircon and you get to mix with some locals. With tickets there is a free transfer to Busch gardens which is ok.
This is handy for an idea of buses in Orlando:
http://www.tripadvisor.co.uk/Travel-g34515-c116996/Orlando:Florida:Bus.Services.On.International.Drive.html
I have stayed in a villa which was good. Nice lot of space, nice quiet area. But the cost of a car was a bit expensive when you have to factor in (at the time) $15 a day parking at the parks! It was ok for us as at the time there was 5 of us so splitting the cost of everything brought the price down but if it was just me and the wife I am not sure I would get a car.
I would think that using the bus and the occasional taxi would be far cheaper. Might not be so good on time but if you are trying to keep costs down I would think that its the best way.
There are some apartments that are called vista cay that are just off idrive. They are smaller than villas so might work out cheaper.
When you get there go to a walmart or something and buy a big pack of bottled water, when I went bottled water in the parks was I think $3-5 for a 750ml bottle and when its really hot its amazing how much you can drink.
Get a small cooler and take some food in, its amazingly expensive in the parks. This can be more difficult in a hotel room with no kitchen equipment but some hotels do have fridges you can have in your room.
Budget Budget Budget and try to stick to your daily budget.
Also get more people to go with you to get the cost down.
There are tons of awesome restaurants to eat at and that can be a large bit of your costs of a holiday. But they are awesome! Olive garden being one of my favourites for a cheap meal Panda Express is awesome, as you might have seen me being tagged in the photos on facebook