I add up what the package costs. Then do it with everything separatly. I find that we don't do the parks on our first day, or the last day. THe one time I did a package (I didn't know any better. Hadn't found these wonderful boards!!), I did go to the parks on my first and last days. The first day I was in the park for about 2 hrs. and the last day for about 2 hrs. So, it wasn't really cost effective. WHen we go in Aug I plan on spending: room (at a mod) about $600-700(7 nights), airfare (for 3), $600, passes (2 4-day hoppers, 1 5 day hopper...we have 2 passes with 1 day left on each and 2 plus visits on each of 3 passes) and then about $800 for food, souvies, and $150 for transport to the resort/SeaWorld via town car service. If I did a package it would cost me about $400 more and I still wouldn't be using all the days I'm entitled to in the parks.
Use the AP for resort stays if there is a difference in what the resort would cost without it (keeping in mind there are some pretty good rates using codes) versus what it costs with the AP. But remember, you have to remember to add the extra cost of the AP to your pass budget instead of a hopper pass. If I use an AP to get a better rate I could save about $150, based on what I'm paying now. But, I'm hoping that a great code will be out and I won't have to buy the AP. Good luck with the planning.