I'll try to answer... someone correct me if I'm wrong - (I've only booked packages, pay in full at the time of booking, and have never had to cancel.)
Some people like to make a "room only" reservation to make sure they get the resort of their choice. This requires one night's deposit. As long as you cancel within 5 days (I think it's 5) of your arrival, you'll get a complete refund. If you book a package, it requires a $200 deposit and there is a cancellation charge. (I think it's $50)
A CM once told me it basically comes down to this... If you are adding $$$ to your reservation, there is no charge, like changing from room only to a package, but if you are downgrading, which means less money will be involved, there will be a cancellation charge.
The difference in price for a room and ticket package -vs- booking room and ticket separately, should be next to nothing, unless you are buying the tickets from an agency other than Disney.
*If you are interested in the dining plan* You can only book the Dining Plan with a package, the package must include at least a 1 day ticket, and everyone in the room must be on the same package. (If one or more in your party has an AP, you will still need to purchase 1 ticket to be consider a package.)
I believe you are correct about the AP and the time of activation.
Only one person needs to have an AP to receive the discount.
With an AP, you can purchase the Disney Dining Experience card.
From what I've read, some people were not happy about the 2008 AP discount.
Some people like to make a room only reservation (with or without a room only discount... AP or
AAA) and then wait and watch for a discount code to come out. If one is released, you can call and have it applied to your room reservation or upgrade to a package, if it is available for your dates and resort.
You can only apply one discount.