Hi Maddielou,
If what I've written below doesn't make sense then ask your teacher or a more experienced player to show you how to clean your flute - it is something which is easier to demonstrate rather than describe.
Dry your flute with a gauze cloth and your cleaning rod.
Polish it with a soft lint-free cloth.
Do not use a silver cloth if your flute is silver-plated - these work by removing dirt but also remove a tiny bit of silver each time, so if your flute isn't solid you'll eventually wear it through to the nickel. If your headjoint or the tube are solid silver you may
occasionally use a silver cloth on the parts that are solid silver (I have a silver-tube flute and use a silver cloth every 3-4 weeks on the headjoint and tube but not the keys/mechanism which are silver-plated - and I play every day).
The pads can be cleaned with cigarette papers, but this shouldn't be done everytime (unless they are prone to becoming sticky) because it puts a bit of additional pressure on the mechanism. Make sure you use the part of the cigarette paper which does NOT have glue on it. Put the cigarette paper under the key you want to clean, close the key gently and the pull the cigarette paper out whilst exerting gentle pressure on the key.
Some parts of the flute can only be cleaned by removing the mechanism, but do not do this unless you are absolutely certain how to put it back together again - I don't ever do this because I'm not confident enough to (and I suspect that I may be more experienced than you). This is something which waits until my flute is serviced.