You will probably receive more than one answer to this.
I refer to God (the one supreme being) as He and use a capital G.
If I am referring to the many Roman or Greek gods, then it is a generic term, and use a lower-case g.
Some people don't like to think about God as being male, but would still not use "It" to refer to God. Instead, they tend to recast the sentence and use proper nouns like "The Creator" and such.