Hey there, Logan.
I don't really know what you mean by "main drive". Usually people refer that way to their OS drive (e.g. the one that has Windows). The way you're planning on doing things, the SSD will be your OS drive and the HDD your secondary storage drive.
If your Windows is on a separate partition then you should be able to clone just the partitions associated with the OS. However if not, you should trim down the data you have on your HDD to a size that's smaller than the maximum capacity of the SSD.
Here's a pretty nice tutorial on how to migrate your OS: http://lifehacker.com/5837543/how-to-migrate-to-a-solid-state-drive-without-reinstalling-windows.
As for booting to Windows via your SSD, you could simply disconnect the HDD and try booting to Windows just to make sure that everything's working properly and that the cloning process has been successful. Once you reconnect the HDD go to your BIOS/UEFI settings and open the boot priority menu. From there make sure that you set the SSD as the first booting option.
Once you're sure that everything is working properly, you can backup the HDD's data and reformat it so that you have a fresh secondary storage drive, where you can install most of your games and keep your files.
Please let me know if you have any questions.
Boogieman_WD