The green peg is to hold the board in place, to make it easier to secure to the other standoffs.
Focus on aligning to the 'peg' and with the IO shield, and everything else should align.
You do not need additional standoffs when they're integrated - if you were to install additional, you wouldn't line up with the IO shield etc.
You'd use the screws labeled "d" in the manual - they're used for both the motherboard & HDD installation. Should be x16 of them included with the case.
If this is a used case and you don't have the included screws, you can test available screws for threading etc.
If a screw fits, and can be secured snugly (yet still be removeable), you can use them. While there's commonly used screws, I don't think there's a...