Well, I´ve booked a vacation (very special for our entire family) with both land and sea.
I´ve talked several times with Disney to try tofigure out what would work better.
I´ve found out (I´m not sure if that is the same for everyone), that booking separate provided me a better deal. Even though part of my travel will be during Thanksgiving (my DD B-day is nov-28 and I figure that travelling at this time would be better, onc seh will indeed celebrate her Bday in WDW and save me a few $ on cake and small "family" celebrations)
I´ve booked both separate, and tried to use most of discount codes, I spend a few weeks quoting prices to check between room only (plus buying tickets and spending money in meals) and full vacation package including tickets and dining plan..
End up that we were 3 (2 adults an 1 child) and the plus on including dining plan would b similar to that I´d spend by eating at regular restaurants - and I´d like to try one signature dinner and (cross fingers) celebrate her B-day at Cinderela castle...We are not travelling during "free dining" time, if you are able to do that it will save you a few bucks.
I´m staying previously to the cruise for 6-night so dining will be part of the trick, I imagine that for 4 night I´d skip dining plan and eat at counter restaurant (too much to see, few time to spend and hour or two in restaurants...). I suggest you to run as much simulation at disney site (use this year to do it, them you get and aproximate amount to 2010) as possible, seek some site discounts for room only on websites edicated to that, call disney yourself and check if there is a discount code for you....It take time, but I think that the $ you save here is worth!!!
After that I did the same with DCL (even called an agent and see if he/she could reduce the cost I´ve managed to figure). They did not. So I booked by myself. Let´s say that for almost a month I spended in planning and booking this vacation...We booked early b/c the way disney handle the payments worked pretty well for us, a deadline for full payment and we can "deposit" as much as we can each month (the travel agency did not matched the price, and wantted a regular payment of the same amount - divided the full vacation for 6 and it would be how much I´d need to pay each month, they did not even get a discount for full payment in advance!!)
I wrote to DCL and adding ground transportation you can be taken either from airport or WDW resort (the only "but" is that not all resorts are part of DCL transporation, but they told me that talking to disney cast there and they provide me transportation between resorts).

So, as we are going to stay in a resort non-participant we will need either to go to airport (using the ground transportation for disney) or go to a participant resort (GF, Poli, AKL....) and them take to DCL transportation from there.
Also I tried different combination between resort and cruise to decide the way it would be better. So by booking in separate you get the possibility of choosing where to stay in both part of the trip. If you choose the "land and sea" package the "level" of the stateroom will be matched to a specific group of resorts....so by separating them you can organize and stay where you want (even using that "secret" stateroom, where there are porthole or verandah and are sold as inside or navigator due to they ´ve not the total view) and them you got a kind of "upgrade"....