I don't believe in God or morals either (because as concepts, they throw out obviously erroneous consequences such as the need to ask this question), but I pay my bills because if I don't they will cut off my electricity. It's nothing more than common sense.
A system has rules, whether they are the laws of physics, a set of mathematical axioms, or the social etiquette conducted whilst having tea with the Queen. The rules are what make a system work, they define it, and the interactions that occur within it.
One thing that the rules have to do is not contradict one another. When rules contradict, we have a paradox. To solve the paradox, we have to either find a new rule, or reappraise our understanding of the rules. A paradox is the point at which a system fails to operate, the point at which it shrugs and starts hinting at infinities, or asks us mysteriously how many angels might dance on the head of a pin. If a system has too many of these paradoxes, it can be deemed to be false. Or rather, the premises on which the system is based can be deemed to be false.
The problem with this question as posed is that it helps prove the non existence of God. It creates a paradox. Did God create Morality, or is Morality something higher than God? Is Morality one of Plato's 'Forms'?
I'd argue for none of the above. Instead, morality (small m) can be best described as a set of behaviours and attitudes that allows a person to function within a society with the optimum ratio of success to effort, and individual vs societical gains. It is a construct of inter-personal interactions that simply did not exist before we did.
Poof. The contradictions disappear.
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