(a) No.
(b) No. SBB only takes your renders and pastes them into a single image, it doesn't manipulate them in any way. If you've rendered it so that the unit is off-centre it will remain off-centre in your storyboard. The way to fix this is to make the flic as usual, and then when it's done open it in Civ3FlcEdit and change the offset. This doesn't cause the problematic Civ3FlcEdit "extra frame" bug so there's no need to worry.
(b) No. SBB only takes your renders and pastes them into a single image, it doesn't manipulate them in any way. If you've rendered it so that the unit is off-centre it will remain off-centre in your storyboard. The way to fix this is to make the flic as usual, and then when it's done open it in Civ3FlcEdit and change the offset. This doesn't cause the problematic Civ3FlcEdit "extra frame" bug so there's no need to worry.