Is it a terry flat, Amy? You can soak cotton flats without any problem, as far as I'm aware... (Soaking tends to coat the fibres of the more modern fabrics and also seems to wear out the elastic of MCNS.)
My nappies do stain, for sure. But they always come out, either after some sunlight or after the second wash. If you use microfleece liners (you can cut your own from microfleece that you can get fairly cheaply) that helps to protect the nappy too, and I find those MCNs I have that have a fleece inner are the most stain resistant.