Does the payload of an Alcubierre drive have to be on board during the preparation phase? I was thinking about the practical aspect of using an Alcubierre drive, assuming one existed.
I'm no expert, but my understanding is that, since the destination has to be in the forward light-cone of the vehicle, there is necessarily a preparation phase.
For example, if you wanted to travel 100 ly in a year, you would set up the drive, point it the right way, let it "warm up" for 99 years, hit the switch, and get to the 100 ly destination in 1 year of subjective time, but the whole process still took 100 years.
Would the payload have to be on board during the 99-year warm-up period in this example? If so would that payload have to be causally disconnected from the region of spacetime which doesn't make the journey? If so doesn't that imply that the destination couldn't receive a FTL response to a message it sent to the vehicle, since the equipment on board wouldn't be able to respond in less time than it takes the drive to warm up?
 A: Would the payload have to be on board during the 99-year warm-up period in this example?
No. The payload does not have to have the destination be in the forward light cone (for the external metric).  And the warm up doesn't happen at the launch site, it happens along the region you will traverse, which is why it takes a while.
The best analogy is the train track analogy.  The coordination of laying down the tracks happens at slower than light speeds.  But this advance coordination could be to bring in exotic matter and put it in front of the warp drive as needed, with a just-in-time type service.  Setting up the coordination of when the exotic matter arrives when and where requires all the advance planning.  But you could bring many possible payloads that benefit from the same planning.  So you can plan first, ship later.
Does that imply that the destination couldn't receive a FTL response to a message it sent to the vehicle
The destination can send a message, and the destination could be the one doing the advance planning and find a payload and bring it back at the speed they planned for.  Assuming they have the exotic matter and put it in place.  
So, to clarify, the "warm up" could start at the destination.
