I found that sometimes they woul dstain the nappies for a bit - usually when they couldn't be dried outside etc. But I have always managed to get them out eventually. If a vest or something has poo on it, i would shove it in with the nappy wash. Nappy san seems to get stains out but I don't use it all the time, just sometimes if nappies are starting to look dull and I want to sell them or something.
I think cotton nappies stain a lot worse than fleece lined ones. I don't really worry if the nappies I have are stained anyway - they are only going to be pooed on again. i recently bought some MEOS for virtually nothing because they were very stained - I am sure after a few dries on the line they will be fine. Haven't made any partiular effort with them though as we only use them when we are at home.