That's a link for a fairly recent discussion about this (if the link doesn't work, try going back a page or two, scanning the topics).
Basically, it just comes down to personal preference. As you'll see from the previous post, I prefer the regular cotton because I like to have the stay-dry be optional (I use fleece); this becomes more relevant when you approach potty-training, and want your child to feel wet. The stay-dry does resist staining much better than the cotton and is a bit easier to get the poop off (fleece offers these benefits, too, but is obviously an extra layer, for good or bad).
Whichever way you decide, there's no wrong answer. ME products are excellent. Congrats on making the decision to go with cloth--I feel that cloth really makes the diapering experience easier and also more enjoyable, as odd as that may sound (until you do it).