We book everything separately. We try to stay at the Swolphin when they have openings, so book that directly to get our SPG points and book our flight (through SW, and my DH flies free on my companion pass) directly with SW to take advantage of said perk. Note that if you book through WDW/Expedia at the Swan for instance, you won't get your SPG points. If we can't get in at the Swolphin, we try the CR and then the YC and will compare WDW rates vs. Expedia rates. For the girls marathon trip in Jan., I saved a decent amount booking AKL through Expedia instead of through WDW direct.
We go multiple times a year for a 3-4 days at a time, so buy 10 day no expiration park hoppers. I'd love to do a longer time at WDW, but DH can only take so much WDW or Vegas, so we hit them more often for longer amounts of time. I know for our April trip, I'd like to hit Blizzard Beach which means we won't do the AK, which is fine, I just did AK with the girls in Jan. and will do it again during F&W. I think this, like almost everything about WDW, is about you and your party travel.