Personally, I don't bother untwisting yarn when working with two colors as I find it doesn't make a difference to my work. However, if you want to try and keep them from twisting in the first place, I would suggest keeping the two balls of yarn seperated by a few feet while working on your project and each time you turn the project, make sure not to twist it. Once you get the hang of that you won't have to worry about the twisting.
As for the granny squares and sewing in ends, I crochet over my ends so I don't have to do much sewing in. When I end one color, I leave a tail and then when I go around with my next color, I just crochet over the tail for a few stitches and then cut it off. I don't really have trouble with them pulling out and I've been using this method for years