Gosh……Where to start ?
As a rule of thumb if I am making a hole and shaft combination of parts I generally make the part with hole first.
Forget using only drills and emery paper, they are for farmers who are repairing ploughs etc.
Make the hole either by drilling then reaming to final size, or by boring it on the lathe or milling machine.
Once you have the part with the finished hole you can then turn the part to the correct outside diameter so it has the type of fit you require.
It is usually much easier to make the shaft fit the hole rather than the other way round.
I will not go into detailed information about tolerances here, but that is what we are really talking about. Rarely do you see any tolerances on average model engineering drawings, usually the article writer will explain what type of fits you are trying to achieve in the text.
From your questions it sounds like you could do with reading up on some basic techniques to get you started.
Dont be put off, it will all become clear…… honest.
Phil