The 2-at-a-time socks book I have says that you will think you have nothing but a big pile of twisted cable, lost needles, and tangled yarn (Wow! I'm really looking forward to that!) - but not to give up - it will all make sense soon.
Another suggestion is to put one ball of yarn in each of two baggies with holes cut in the corners to pull the yarn through so that you don't get the two yarns mixed up. That sounds like a plan to me!