I just take off what I can with a bit of loo roll, dump it down the loo and dry pail the nappy. I wash every 2-3 days, and haven't had stains yet. Ds2 is very good at shifting the fleece liner I use too so it never hits just that either! I wouldn't worry, and if it does get stained, just put it out in the sun wet, and keep damping down the stain when it dries and the sun will bleach it out
When you put your nappies into the machine to wash, just use a cold rinse cycle first to rinse off all the poo then wash as usual, the hot wash will make the nappies stain but the cold rinse will get rid of the poo before it sets the stains in deeply iykwim.