1. Each time you want to execute your any Special Order, you have to put it there after that (but there are some exceptions). You cannot put there more SO than # of your R&D modules during single round. When you are not able to execute SO, you discard it, taking an Event card instead.
Thanks to new rules for SO you are able to use them even in 1st round (unlike without expansion).
2. It stays there as long as you: control the area OR you use it at the start of the battle in the area. When you didn't use Guard token, it is checked if you still control the area immediately after a battle is resolved.
3. You still must obey unit limits. You destroy transports or routes where any units are moved to the area with Air Support module.
4. Yes, it's allowed (at least: there is no rule forbidding that). You may use own rules if you don't like it.
5. Just read rules on that technology card. # of Arbiters doesn't matter (if iI remember well).
6. During "Draw Combat Cards" Battle step, the defending side also draws card(s): 3, if you're playing Protoss, 1 if you have other race. When you are out of Combat cards in hand, you are forced to play it directly from deck (without looking at them), 1 for each skirmish. It's rather a rare sight to be OOC...
7. Yes, but after ALL skirmishes are resolved.
8. Well, there are some ways to avoid this, but you have to put your orders (and starting transport) with ready plan for your first turn.
- try to escape to another adjacent planet to build a base there (but you don't have to) and to counterstrike invading forces in the same turn, at least you will keep a base in some safe place
- remember you may upgrade your base (building or module) even if you don't have a base on the active planet
- exploit that you reveal your order earlier than your oppotent and attack him first on his homeworld, "Attack is the best form of defense" ^^
9. Only after you played specific Stage III Event card: "Inspiring Leadership", which allow to activate second Stage II LC.