I've done this pretty much every way you can. I prefer buying a 3 or 4 day pass, using the MM option, then transferring to APs on the final day of the ticket. It just feels like it gives you a little more bang for your buck, especially if you want to go during a time when your pass would otherwise be blocked.
In terms of buying at the parks or online, I choose online. It's slightly faster. You still have to go to the ticket booth at some point during your day and as of last November, their computer system was still slow and it took longer than it could have with a better system, but at least they had all of our personal information already so they didn't have to ask us to write down all of our addresses, birthdates, etc.