Flute Care?????????????

I just recently bought a yamaha flute for my marching band at school. I've never owned a flute before, I just rented from my school. Now my question is, on the manual thing, it says not to put the cleaning cloth and polishing cloth on top of the flute when its in its case because the cloths can cause unecessary pressure to the keys and damage them. So basically, the only thing that should go in the case is the flute and the stick thing. So my question: Where are you suppose to put the cloths then? Thanks.