I use old mandrels (thick ones) to mix. That way I can control the amount of glass that goes into the color. If you just use the rods, it is hard to reproduce exactly. I used shorts mostly and punty them to the mandrels, then twist and twist and mix and mix until all one color.
Darn it, there was an excellent post on the old ISGB forum that described a great way to mix glass. I found a post I made with a link, but couldn't get the thread.