Normally the motherboard comes with a small standoff already installed but when I bought my board it came with an m.2 screw and a longer standoff. You take the standoff and you install it on the already installed standoff on the motherboard. This should bring the standoff as high as the m.2 port on the motherboard. So the m.2 will stay horizontally seated on the standoff. Then you use the m.2 screw and you screw it in the standoff on the board.
To know if a SATA port is disable you will have to look in your motherboard manual.
View: https://imgur.com/a/Q3bj1qG
You can see the already installed short standoff and you can see at the left that another standoff was added on top to make it higher. So it's 2 standoff on top of each other.