Boot disk doesn't have to be on sata port 0, it can be on any sata port. You would go into the hard drive selection, and choose the model of the hard drive you want to boot first, or in new machines, you would have an HDD boot order section, and you would go into there, and set the order for the drives to boot, obviously if the drive is not bootable it should be placed at the bottom of the list, or deleted/skipped in the list.
And yes, you can delete the old windows directory, it will not be needed unless you want to keep it there, in case something were to happen with the new boot drive, you can revert back to the previous drive, and be back up in just a few minutes. If it is the same windows license, and you are worried about that, don't be, the license allows it to be loaded on one machine, it's still the same machine.