That's if you have an onboard graphics chip on your motherboard. If not, then you can install the graphic card straight away. If your motherboard does have an onboard graphics chip, then what you do is install the graphic card into it's slot, go into the BIOS and disable the onboard graphics. If there isn't an option to disable that in the BIOS, then you'd have to disable it once you finish installing the OS. Then you would have to get to the device manager in the control panel and disable the onboard graphics there. And then continue to install the graphic card's drivers.
The standoffs are there to separate the motherboard from the case's metal. It is most importantly preventing the solder points from the back of the motherboard from having direct contact with the case, which would have the motherboard malfunction if it did.
A toroidal choke or coil is this:
Who said you would need it? You would see a few of these on your motherboard by the way. And when building a computer, you do not in any way have to worry about toroidal chokes/coils. Unless you see a motherboard with bad damaged ones, in which you would have to RMA the motherboard.