[EDIT: Didn't realise this was an old thread!]
I always book accommodation and park tickets direct with Disney UK (always stay onsite). I used to book the flights as part of the Disney package but since I've become a member of Virgin Flying Club and accumulating points from previous flights, credit card and Tesco Clubcard, I've booked flights separately with Virgin Atlantic. That means I'm not ATOL covered though. This may change in the future though since I've more-or-less stopped using that credit card (for various reasons),and I may go back to flights with Disney.
I'm sure it's cheaper to buy the accommodation from Disney and flights from the airline separately, otherwise you pay a premium for Disney accommodation from the third party travel agent or the flight when Disney is acting as the travel agent. But you also have to weigh up convenience and, in these days, how easy it would be to change or cancel and get refunds.
I prefer to go in February and November and usually have a particular Disney hotel in mind. Bearing in mind Disney releases accommodation packages in March/April and Virgin releases flights around 11 months in advance, this can dictate whether I buy hotel first, flights first, or both on the same day. The hotel I want might not be available for the dates I want on release in April. And if the dates I want are in November the next year, the flights won't yet be available. If you're willing to take it to the wire, of course you can book for the same year, but if you want a particular hotel then it might be advisable to book as soon as it's made available because the "stock" that Disney UK has is limited and can change a lot as time goes on. So as to timings, it all depends how flexible you are as to dates and hotels, and flight prices are also unpredictable so it might pay to wait until you find a date when the flights are reasonable then fit a hotel stay around that...and book both on the same day!