I'm gonna go back to a tweaked version of Leibniz's explanation on the whole God thing.
Every contingent thing has to have a cause. The cause has to be either another contengent thing, or a noncontingent thing. Matter, itself, seems to me to be a contingent thing -- it doesn't _have_ to be there in any capacity to cause something.
If a contingent thing caused something, then the contingent thing itself had to have a cause. So there's two possible chains of events. (arrows represent "caused by")
(an infinite chain of contingent things, or "turtles all the way down")...<-contingent thing<-contingent thing<-contingent thing<-contingent thing
(an arbitrarily long chain of contingent things caused by a noncontingent thing).noncontingent thing<-contingent things<-...<-contingent thing
The question, then, is "is it the case that the universe has simply always existed, or did it come into existence at some point". Thermodynamics seems to empirically point to the idea that the universe was created at some point, which means that at some point no noncontingent things existed. It's the question of a first cause.
If you can find a loophole and reverse the second law of thermodynamics (causing entropy to decrease), then it's possible for the universe's existence to be that noncontingent thing, and simply have always been.
As for what theists think about God and Free Will, there's so many possible explanations that make the concepts compatible. Like I said, you can just be a nondeterminist like Berkeley, or you can wave your hands about the Compatibilism doctrine of Leibniz and other determinists or employ another soft determinist technique.
The thing about free will is, if you view the mind as a pure machine, then there's no possible such thing. If you view the mind as something beyond machinery, and equate what thinks in us with a soul (removing it from the realm of determinism), you can still have it even in a deterministic universe with an omniscient god.
But if we're nothing but very complex deterministic machines, and that includes the mind, then the whole concept of free will is completely pointless.