Boy, this is a big topic -- I feel a lot of responsibility answering this question! Everyone else chime in please.
I've seen them three times.
The first, at the Metalfest, they were sloppy. The vocals were a little unsure. They themselves admit they don't rehearse much. But it was such a thrill to see them that it hardly mattered.
The second time was at a local club with Nevermore. It was damn near flawless. In fact, I heard no flaws, but there must have been some.

They were miked
perfectly. Every single song was perfection -- just not long enough, of course. About 45 minutes.
The third time was at the same club a month later with Amorphis. That time was actually rather disappointing. They were miked poorly -- what a difference that can make! Couldn't hear Mikael very well. And they were a bit sloppier that time.
As for logistics, I couldn't tell you what gear they used. I don't know much about that stuff. Hopefully someone else can tell you. They don't use acoustic -- instead, substituting clean. So obviously it's not as finessed as the recordings, but it's still Opeth, if you know what I mean.