While your baby is exclusively breast feed, washing diapers is rather easy. Just take the diaper, BM and all, and toss it in the washer for a cold rinse cycle followed by your hot wash routine. Breast milk poo has the consistency of yogurt and will easily break down with just water.
Once you introduce solids to your babies diet or start to supplement with formula, your diaper washing becomes more complicated, but still manageable once you get a routine down. At this point you will need to remove the waste into the toilet before washing the diapers. The easiest method that I have found is to use a "diaper sprayer" and spray to waste into the toilet. I keep a bucket beside the toilet to store that diapers in. When I have enough diapers to wash, I do a quick cold rinse cycle to remove any lingering stuff and then do my regular wash routine (see older posts for delated washing instructions. A diaper sprayer is a device that is connected to with water line and your toilet. It looks like a hand held bidet. They are available online and at local diaper retailers. Here is a link for more information: http://www.minishower.net/
There are several brands that are similar to the one in the link. This is the brand that I use. If you don't have a diaper sprayer, nor the funds to purchase one (they cost almost $45 new, I got one on craigslist for less than half that price still new in package) you can still effectively clean your cloth diapers. When your baby is older waste may "plop" easily off the diaper into the toilet, while they are still young and poo is more of a "peanut butter" consistency, you will need to do some dunking/ flushing to remove the waste. Rubber gloves a good for this, keep a pair near your toilet that are just for diaper dunkin'. Remember to keep a good grip on your diaper, you don't want to flush one down! Another useful tool for dunking to clean is the diaper duck, here is a link: http://babyworks.com/cloth-diapering/diapering-accesories/diaper-duck.html
I have never used a diaper duck, but they look great. This will ensure you don't flush that wonderful prefold down the toilet.
To remove stains from diapers make sure to do the initial cold rinse. This will remove the poo residue and won't set the stain. The best way to remove stains is to air dry your diapers in the sun. The UV rays work wonders on diapers. If you have no sun (hey we live in Washington State) then you can use a tiny bit of bleach in your wash once a month or so. This will help to disinfect your diapers as well, especially if you are getting a lot of ammonia smell to your diapers. You can also try using a non-chlorine bleach like Oxo-brite. This is an oxygene bleach that I get at Trader Joe's. I love this stuff, it works great. Now that I use Country Save detergent, I don't use Oxo-brite as much because Country Save already has oxygene bleach added to it. Check your detergent, if you don't have any "sodium percarbonate" in yours, try adding a scoop of Oxo-brite or Oxyclean Baby to your diaper wash. It may work wonders. Lastly stains don't usually mean that your diapers are not clean. Smell your diapers, if they smell like nothing at all or smell clean, then they are.
If you have questions or need more information about cloth diapers or washing cloth diapers, email me or send me a comment. Happy diapering.