Migration Assistant
So, I am looking to buy a 1TB Fusion 21.5" iMac and I was planning on splitting the OS 500GB Windows and 500GB OS X. Can I get the windows migration assistant to transfer my files to only the Windows half of my Mac or not?
Your Fusion drive will need to be partitioned with Bootcamp Assistant and the Windows part will be only on the HDD. The 120Gb SSD and remaining ~500GB of the HDD will become a CoreStorage volume which should have OSX on it. Please see About Windows Migration Assistant - Apple Support for it can migrate from a Windows PC. This will migrate files from Windows to OSX, not Windows.
Once Windows is installed, you can migrate files between Windows using Windows Easy Transfer. WET does not transfer applications. You will need to re-install applications using the original installation media for such applications. If you want to migrate from Windows on old Mac to Windows on new Mac, boot both Macs into Windows and use http://windows.microsoft.com/en-us/windows7/products/features/windows-easy-trans fer for such migration.