Perhaps the BEST B1G Forum anywhere, here at College Football Fan Site, CFB51!!!

Anyways, like I said, I was pretty confused the whole time for S2. 

I couldn't really figure out WTF was going on with Gemma? 

She's being held hostage in the floor below the regular severed floor.  They take her into various rooms where separate innies are activated for that particular room.  So unlike the severed people we're familiar with who only have one innie, Gemma has a slew of different innies.  Each room is a stressful or unpleasant situation.  Presumably Lumen is testing to see that the severance technology holds up under stress and that memories don't bleed through, and may intend that to be a main function of the implant (like the senator's pregnant wife who didn't feel like going through childbirth, so she made her innie do it).  But that's a bit speculative at this point.  Each of the rooms she goes into have names that correspond to files Mark S has completed throughout season 1 and 2.  Indicating the numbers he quarantines may somehow be memories, or maybe personality traits that are being removed for each room's innie.  Don't overlook how the 4 categories the MDR team classifies the number clusters into are the same 4 "tempers" Kier identified in his work.  (They're also represented by the 4 dancers in that hyper-creepy scene from Dylan's waffle party.)

And what was the deal with the little asian girl? 

They don't specifically say, but they do say she's trying to get the same "fellowship" or whatever they call it that Cobel/Mrs. Selvig got when she was a kid, as revealed in her backstory episode.  The doctor lady who was helping Mark on the outside to re-integrate once said about Cobel "They raised her, she's Lumen through and through."  That seems to indicate whatever's going on with this Asian kid.  Like Cobel, she's being groomed to be a true disciple, and probably shows a lot of promise, since that fellowship is supposed to be prestigious, it seems (according to Lumen).  

Were they trying to reserruct Kier, and what did goats have to do with it? 

I think it's heavily indicated, though not yet explicitly stated, that The Board is Kier and his descendants, although how and where they're still alive, I don't know.  Maybe their consciousnesses are stored in a severance-type chip.  I don't know if they're trying to resurrect them into new bodies, but that seems plausible.  They haven't explained the goats, other than just as some kind of sacrificial offering.  There's a ton of fan theories about that, but I don't think the show has explained it.  

What was supposed to happen to Gemma? 

The creepy doctor was told when Gemma completed the Cold Harbor room, he would have to say goodbye to her.  It wasn't clear whether that meant they would kill her, or delete her original personality, or if it just meant that he wouldn't be able to see her anymore.  She asked the doctor herself what would happen to her when she was finished, and he told her "You will see the world.  And the world will see you."  Lots more fan theories about that too, but again, it hasn't been explained yet.  

You mentioned you frequently don't watch closely, so I have to ask, how close were you paying attention?  You've got a lot of big things right and a lot of the smaller details wrong. 

With Gemma, at times it seemed like her outie was present. She knew she wanted out, but when she attempted to leave, her mind would pass into her innie. I guess I didn’t completely pick up on the multiple innie situation, it sorta seemed like she was zombiefied.

Anyways, like I said, things seemed to skip around a bunch. I may rewatch S1 and 2 just to try and keep up with everything.

Re: Severance - Gigem

I'm going to try to keep this as concise as possible, and Mike already did a good job of addressing most of your posts. But first, I'll pile on and say half-heartedly watching the episodes cannot lead to a full understanding and appreciation of the show. There are multiple instances where a line or two of dialogue provides a great deal of context going back (or forward) several episodes, even across seasons. The use of color (blue, red, and purple) creates a theme throughout the show. The use of sound, or in one specific instance, the lack of sound provided a significant clue to what is happening.