I recommend only having the SSD connected when you install Windows. After it is done, shut the system down and then connect your other drives. Windows Setup has at times written the boot information to a different disk than the one you have chosen to install the OS onto. This might not seem like a big deal at first, but down the line if you need to replace/upgrade the disk, your OS may not boot. Also, there are certain situations which would cause the "wrong" disk to be enumerated first by WinPE, meaning you could install your OS to the wrong disk by accident. Only having the one connected at install solves both of these potential problems.
Retail box motherboards should come with 1-2 SATA cables for you to connect your disks. I can't speak for everything, but both Asus and Super Micro retail boards come with 2 cables.