Try not to use your hands unless they are completely clean. Some nets are more rough than others and can cause problems with finnage getting caught. If you have his cup still and you can scoop him out then do that. Using a net though is still okay, just make sure you rinse it under a running faucet of hot tap water before and after each use.
Doing water changes you want to do 100% every day.
I use 1 whole cap full every time i do a water change in my 1 gallons while fish are being hospitalized, if you at all feel like that's too much you can use half a cap. I have never had any problems using a whole, but it's up to you completely.
If you live in an area where there is a WalMart then you can find 1 gallon diamond tanks for $10. They have a hood with a light and a bubbler, you won't need the bubbler but it's a steal to get it all for that price.
Keep an eye on the tank temperature with that heater in it. If the heater isn't supposed to be for that sized aquarium i've noticed with my fish they start freaking out. I don't know if it makes a noise or vibration in the water that bothers them or what, but they tend to like, spazz out. If you notice this at all just take the heater out.
If you don't want to buy a hospital tank or are unable to (anything that's about 1 gallon should work, you don't always need to have it be a tank just so long as you never use it for anything else) you can always just lower the water levels in your aquarium like Virto said. Remove any and all gravel and give the tank a nice hot scrubbing under running water. Keep a plant or two in there so he doesn't get stressed out.
I've never used Maracyn Plus but that should work okay for the eye problems but it doesn't look like it will help with the body fungus.
Look for this next time you go to the store: