I know how this works actually. It's the reason why Stoke's allocation was supposedly increased by 2000 a few weeks before our final with them.
If you take out the middle tier, the stadium is divided into two. But a number from each side are ring fenced for the FA for member clubs, sponsors etc. When you apply for an FA ticket through that scheme you have to tick which club you support and they allocate them on that basis. If any aren't taken up, like Stoke's 2000, they then go to the clubs. I got a ticket for the Wigan final using that method through a mate who works for a premier league club. They could apply for up to 6 I think, and I got 3 of them.
If you remember, I said that this had happened on the first day of sales. I know because I bought tickets in block 120 on the first morning, but a whole square section in that block were already unavailable.