@Macsure: This is just the best answer I can give off the top of my head, and only because I’m bored and waiting for a reply to this topic, so plaease don’t take this as scripture or help from the far more experienced admins. That being said…
From what I understand, there is not as of yet a industry wide standardized motherboard color coding format for various SATA type ports, speed or controller type. You’ll need to get the spec sheet on your particular motherboard and make sure you have your SSD/s plugged into the Intel controlled SATA 3 slots.If you have trouble finding the spec sheet the admins here are usually wizards at finding it. Again, this is an outsider’s persepctive, I’m not making any claims as to what they can or can’t or will or won’t do. But it’s probably true if you ask nicely, they’ll help.
Also, if you have more than one harddrive with OS’s you’ll want to make sure the harddrive you want to run Windows is actually doing that. (It’s unliklely that you’ll have more than one OS at any time, but there are certain reasons you might. For example, following the clone of my old harddrive, I had two with an OS.) There are a few ways to do this.
In my case, after the clone of the old harddrive, the only useable SATA 3 slot is in position 3 on my motherboard. (My guess is the architects of my motherboard never intended the SATA 3 slot to be the primary data port position but rather an extra data storage slot.) So I had to switch my SSD to the slower primary (SATA 2) slot and format my old harddrive so that when the computer boots it gets past position 1 (the original harddrive, which is now just a slave sotrage drive) and goes to the only OS which is on the SSD.
Hope that helps a bit. Good luck to you.