We book with Disney direct as this works out the cheapest - you can book packages with or without transport so you could compare the prices. If you manage to get a good deal on a flight you could book that separately and get a without transport package from Disney.
We go on Eurostar and find it's a bit cheaper to get the room & park tickets package and then book Eurostar separately.
Depends on where you like to stay.
At the Disneyhotels you can only book packages (and you only get the 3=2/4=3 discounts) or you have to have an AP.
The selected Hotels like Holiday Inn or Kyriad are often cheaper (look at my website) and then you can either buy AP´s or a 3day hopper ticket.