I used cloth diapers with my daughter and had only a few stains that didn't come out. First, I too used the little liners for the pooh. I also rinsed the dirty diapers out in the toilet. Then in my diaper pail I let them soak in a solution of water and Borax (very inexpensive, and I believe it has directions on it for diaper pails and washing diapers). I washed in HOT water w/ Dreft, Borax and Biz. I also hung them out to dry (the sun does bleach them). I also, if they were still stained, made a paste of all three, water and just a little bleach (not enought to irritate the baby) and rubbed on, let it dry and rewashed.
I hardly had any problems with stains with this method. My mother used cloth diapers with my baby brother and I learned the tricks from her.
Hope this helps,