Did they intend to coordinate with the soviets? Was a target list ever prepared? Did the USAAF spare German cities from bombardment to preserve them as "test cases" in the way cities in Japan were?
There were no real plans for bombing Germany with the atomic bomb in World War II. Concrete planning of the sort you are discussing (target lists, spared cities, etc.) did not really begin until the spring of 1945. The first real meeting on targeting was not held until April 27, 1945, which is to say, three days before Hitler's suicide. Preservation of targets, etc., all followed these meetings.
Separately, you might this post on whether the allies would have used the bomb on Germany — if it were available — useful/interesting. But the schedule alone meant that this was not seriously contemplated.