Basically, when I used to buy a new hard drive and use it as the boot drive and reload Windows and such, I would just place the current hard drive as a slave and pull whatever data (downloads, pics, video etc.) off it when I wanted to instead of copying all the files to the new hard drive. But, that's when I was just using a single drive.
You do basically the same thing.
1.) Create your SSD RAID array and install Windows with no other drives connected.
2.) After you have Windows installed make sure that your SSD array is the 1st boot device in your BIOS settings, connect your HDD array and boot into Windows.
3.) Windows should assign a different drive letter (D: ) to your HDD array. Copy any necessary data to your C: drive.
4.) Reboot into BIOS, delete your HDD array, and create a new one. That will delete the O/S and all data on the HDD array.
5.) Reboot into Windows, initialize your HDD array, assign it a drive letter.
6.) Move the data you copied to your C: drive to your HDD array.