I would basically take care of using them at only the same time so as not to alert the leadership of my enemy. I would bomb mostly capitals where the political leader was with the exception of Hitler or Mussolini. In those cases, allowing them to remain in power proves much more useful because they alone destroy themselves with poor decisions and to have them replaced with somebody capable would extend the war effort unnecessarily. Basically, this is why Hitlers home was never bombed.
In the case of Germany, the bomb would be dropped on the Ruhr
For Italy probably wherever the Italian fleet was anchored since the Italian army is useless.
No bomb could be available before 1944, but if i was Hitler, dropping it at the Normandy landing would prove some advantage and postpone another landing for a year. The other 5 bombs could go against Soviet cities and London as well as the ports where the allies were staging for Overlord.
As Japan, bombing Hawaii and Panama would be useful.
All of these measures would not in itself force the Allies into peace IMO. The Soviets might collapse but only if it was available in 1941-42.
Once the war direction was obvious, such measures only postpone the same conclusion. It could only help the axis if they had it earlier, which begs the question that the Axis should not have started a war until 1943.
But if the axis had and used such weapons, you might expect many more assignation attempts against Hitler