My new mac has two drives. Will setup assistant transfer files correctly?

My new iMac has a hard disc drive and a solid state drive. Does setup assistant transfer files from the old Mac to the new one by placing the files on one drive or on both? With setup assistant can I designate the SSD as the destination for transferring applications and the HDD as the destination for documents, music, photos, movies, etc.?
After completing the transfer with setup assistant will I have to move applications from the new iMac's HDD to its SSD?
Will the setup assistant have any effect on Lion in the new iMac?

That's helpful. Is there any impact to quality? It's not practical for me to USB or Ethernet it, since I don't have adapters and storage, etc. It is, however, convenient for me to let the laptop sit for a day (the estimated time) and just take in data at it's own pace on Bluetooth.
Is there going to be any loss of quality using this? Choppy songs, etc.

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