I haven't done the land/sea cruise package since they added ME to the mix.
When I went, you made the resort part of your cruise package and you were transported on all three stages on the
DCL cruise buses (airport to resort, resort to cruiseline, cruiseline to airport). I guess now that ME is part of the mix, part of the trip is on ME buses. But it should all be included in your cruise package costs.
What is also nice is that if you do the DCL package, the cruise check-in at the resort is significantly shorter in time, because there are only a few people checking in from the cruise line package, as compared to just the resort package.
But with the new online check-in, that should go fairly smoothly now too.
And definately do the resort portion before the cruise; that is what I always did. If you do the resort after the cruise (like friends of mine) they regreted it, because they were too exhausted from the cruise to really do the parks.