What version of Windows are you trying to install? You need to have the Windows install disc copied to the USB in such a way that the USB is bootable. For Windows 7 Microsoft has a tool you can use to do that, I think it also works with Windows 8 but I'm not sure. You will need to either go into BIOS and tell it to make a USB drive the first boot choice, or hit a key (if your motherboard supports it) during POST to select a boot device, and at that point tell the BIOS to boot from the USB drive.
Once you boot the Windows install disc from the USB drive it's just a matter of telling it to install on the SSD. However, if I were you I would first disconnect the HDD with the OS already on it. Windows has a habit of installing the boot loader to one drive and the rest of the OS onto the second drive. Then, later when you remove what you thought was your spare drive (or it fails and is replaced), Windows will no longer boot unless you know how to put the boot loader on the OS drive. Avoid all that and just disconnect the HDD until Windows is installed on the SSD.
Thanks for the help, yeah I have the USB setup as a bootable USB, used it to install Windows 7 initially onto my HDD.
I'll give it a try of unplugging the HDD and leaving the SSD in. When I was changing my boot options, in the boot loader section of the bios I only saw that I could pick my SSD or HDD, I'll double check.