I would also book everything separately, unless you just don't have the time or enthusiasm to do it.
If you want the flexibility of going in & out of parks whenever you want then you should go with the lengh of stay type ticket or Ultimate Park Hopper as I think they're now called. If you want to save a little extra money on the tickets then go with the 4 or 5 day hopper. It's not as flexible, but if you don't do a park for a day you don't feel like you've wasted a day by not using the UPH. Park Hopper days never expire.
You can book airfare through some major carriers 11 months in advance. If you will be travelling at peak time then my recommendation would be to book as soon as possible. We've had the best luck with rates the earlier we book. If you want to wait for a Southwest or JetBlue fare you could possibly get a better rate, but not necessarily. Their rates come out comparable to what the going rate for that time of year is.
Start saving for things now. Save all your change, save dollar bills, start buying Disney $'s. It may not seem as though these things will matter, but you will be so glad to have some extra cash when you are ready to go - whether it's for souvenirs, a special dinner or breakfast, snacks in the parks or even to possibly upgrade your hotel.
While we always get a car, if you stay on-site you don't necessarily need one, thus saving on car rental - although you'll need a transfer to your resort.
There are many ways to save. I'm sure you'll get great tips from the people on these boards!
