It's not a good idea to clone a hard drive to an SSD. Do the windows install directly on the SSD. Also, in order to make life easier down the road, make sure the SSD is the only attached drive when installing the OS. You can attach the rest of the drives after installing windows. This will guarantee that the boot loader and the OS end up on the same drive.
I read somewhere that's the way to do it.. anyway, I guess you are right
Install Windows on the HD with the entire drive used as the partition. When you get the SSD, install a clean copy of Windows on it. Next, just delete the Windows folder from the old HD, and use it for data storage.
Sounds like a plan!