I plan to purchase a new iMac with Fusion Drive. I currently have a Mac that has a 250 GB flash drive and a 2 TB hard drive and use Time Capsule to back up both drives. When I transfer this data from my Time Capsule to the new computer will it know to take all of the data from both drives?
Only the data from the startup volume will be transferred automatically by Setup Assistant. The rest you'll have to do yourself. One way is to start the old Mac in target disk mode and connect it to the new one with a FireWire or Thunderbolt cable.