Hey there, crosbycail!
You should always perform a backup of your data, before tempering with your storage devices!
It's highly recommended to perform a clean/fresh install of the OS onto the new SSD. This is the best way to avoid the migrating of redundant OS files that would bottleneck the performance of your newly acquired solid-state drive. However, in order to do this successfully, you'd need an OS installation media or a bootable USB drive that holds your OS version and you should also make sure that the HDD is unplugged during the installation of Windows onto the SSD.
Here are a couple of tutorials that can tell you more about HDD & SSD optimization:
Win 7 -
http://www.overclock.net/t/1156654/seans-windows-7-install-optimization-guide-for-ssds-hdds
Win 8 -
http://www.overclock.net/t/1240779/seans-windows-8-install-optimization-guide-for-ssds-hdds
Keep in mind that since the HDD was the previous booting drive, you'd need to reformat it and reinstall the software.
As for the cloning, there are a number of programs you can use. Since you'd be cloning your WD drive, I'd suggest you try Acronis True Image WD Edition. The manual clone will let you select the specific folders that you'd wish to have on the SSD besides the OS.
Here's a link to the software:
http://products.wdc.com/support/kb.ashx?id=uA858l
A tutorial on how to perform the manual clone:
http://products.wdc.com/support/kb.ashx?id=St9wyc
Either way, you should reformat the HDD and the software on it. Once you are booting from the SSD, it's very likely that the games and some other software apps will struggle loading/performing. So I guess, you could say that this part is inevitable.
Hope I was helpful. Keep us posted if you have more questions!
SuperSoph_WD