@mrfluke: This year is really the first time they've had a dedicated autograph area. I would assume it's limited to one or two items. Might be a good question to ask @official_pax via Twitter. Let me know if you get a response.
@alwaysbeclothing: You aren't "allowed" to line up until the line for the previous panel goes inside, which in this case would be just prior to 6:30 PM. Now, as @breakfastking mentioned, there is somewhat of an art in loitering around in the area of where the line will be prior to the "allowed" time. If you want a really good seat, you need to be ready to jump in the official line right as that previous panel's line goes inside. If you don't care about being up front, you should still probably get there not much later than 7:00 PM.
@bacongames: The major difference is that most of the theaters are not even in the convention center. If you look at the names of the theaters on the schedule, there is a sort of a secret code to knowing where they are. The first letter of the theater name tells you what building while the type of animal tells you what floor. Sound crazy? Well...
Hedgehog - Hyatt - Ground floor
Sandworm - Sheraton
Sasquatch - Sheraton
Sphinx - Sheraton - Level 3 (they fly)
Wombat - WSCC - Lower
Wyvern - WSCC - Upper
Here's a map from a few years ago to give you an idea how far certain places are. The farthest is easily Benaroya. They are using it as the Main Theatre again this year. It's a symphony hall that was also used for the TI3 Dota tournament last year.
Long story short, you're probably going to spend a lot more time outside than you do in Boston.