I doubt they would stain your nappies - has never happened to me with my multi-coloured ones. I always use fleece liners with pocket nappies - easier to dispose of poo & helps prevent staining to the fleece on your nappies
I use fleece liners in all our nappies - fitteds, pockets and AIOs! There's no reason why you wouldn't be able to use them in pockets...?
They are good as they keep bums feeling drier and also protect the nappy from nappy cream and of course poo - typically, the ONE time I didn't use a liner in one of ours, DD pooed and it stained the nappy with fleece liners it's easier to dispose of the poo in the toilet too.