Engine Overheated Then Started Knocking Really Loudly :/

Well it could be that you've already done the damage and starting it back up is the only way to find that out. Sometimes overheating in itself will produce weird noises. Your thermostat for instance could have been "popping" open and closed (binding) making some of that noise. It also could have been that your cylinders were so hot that your fuel was preigniting. First will it still rotate? If so you'll need to start it up again paying attention to your oil pressure and looking for any smoking. Of course if still knocking or if smoking you'll have your answer. Even if it doesn't seem that there is any damage I would also do a compression check to see if you possibly warped a head and blew a head gasket. Check for water in your oil and or bubbles or oil in your coolant.

No need to drain anything yet. Pull your dipstick and look at your oil, to see if it looks milky or has any abnormal look or smell to it. Check your coolant for any floating drops of oil. When you start it up, pop the radiator cap before it warms up and look for any continuous bubbling ( you may even get a slight smell of exhaust with the bubbling).

Compression check is fairly easy and you can rent a compression gauge at autozone for free. Remove all of your plugs and thread the compression gauge hose into the spark plug hole. Crank the engine several revolutions until the gauge quits increasing in pressure. Write down the pressure and repeat for each cylinder. Your looking for low pressure in one or more cyls. Compare them all and see if any are a lot different from the others.
Low pressure in one or more with continuous bubbles in the coolant would be blown head gasket between the cyl and water port (or cracked head or block)
If two cyls that are next to each other have low pressure then that would indicate a blown gasket between the two.
Low pressure with continuous smoking out the exhaust would be bad rings.
If the exhaust smokes only at start up but then goes away that would indicate bad valve seals

No way to bring back bad fuel but depending on how bad it is you could siphon some out of your tank and mix fresh fuel with it. That is if its not real bad. Does it have a varnish smell to it? You can and should also get a can of seafoam and mix some in your tank to clean things up.