I guess my first suggestion would be to backup all the data from your drives before proceeding with the re-configuration.
If you already have the OS installed on your SSD, I'd say that most of the hard work is already done. It is recommended to format your HDD if it was previously used as a boot drive.
I'd suggest to check out these links: http://www.overclock.net/t/664738/how-to-setup-ssd-boot-drive-with-secondary-hard-disc-optimization
As for using your HDD as a secondary data drive, you can simply change the dafault download location to your hard drive:
Hope this helps. Keep me posted if you have more questions!
So for example farcry 4 is installed on my HDD and I wanted to play it without moving it to the SSD would it work.
As long as it was installed after you've set the SSD as a boot drive, you shouldn't face any difficulties.
Otherwise it's not certain that it will work, you should re-install the software apps after re-configuring a new OS boot drive.