I've worked from both ends of the same ball and from two different balls, and noticed that using two usually results in LESS twisting together, but it won't eliminate it altogether.
Normally I'll work from both ends unless I know before I start that I'm going to use multiple balls. I'm not a fan of joins (actually it's weaving in ends I'm not a fan of) so I try to avoid having a bunch of partial balls lying around. If it's only going to take a single ball, I just use both ends. That way I have one big ball rather than two little ones when I'm done. (Oh stop it, GG!)
As for how to avoid it, you'll never eliminate it completely. But if you notice that one particular movement is producing more twisting than the others, you might be able to compensate as you go. And depending on the yarn you're using and the pattern you're making, it may not matter if it twists together or not.