Setting up Disk for Cloning

I recently purchased a 250GB SSD for my desktop computer as my main drive. I had a 1TB hard disk already in there that I now plan to use as my primary data storage device. I noticed it had the System Reserved section on it in addition to the single volume which constituted the rest of the drive, which I don't need anymore. I went ahead and formatted the drive, but if I remember correctly, I think I came up still showing the System Reserved portion. I think I then did a "Clean up a disk" command and an initialize command and am at the point where the disk is showing unitialized. The problem is, I'm missing about 70GB out of this 1TB disk, as I'm only showing around 931GB, which is about the size of what was the System Reserved section. How do I recover this section so I can use the full drive? And once I have done that, I want to split it into two drives, with one about 250GB in which I want to clone my SSD, and use the other portion for data storage. First off, how should I format these partitions, do I set the partitions up as primary or logical, and will the cloning process clone the System Reserved section on my SSD to the partition I have set aside or do I do that separately somehow?