Actually Nagasaki posed a severe targeting problem. The Mitsubishi steelworks were in a little cup in the earth. If the bomb missed by too much, the blast wouldn't hit the plant. But yes, it was decided early on to maximize destruction by the two weapons in order to shock the Japanese into surrender. Remember: it was partly bluff - if they didn't surrender after the second bomb, it would be a year before enough Pu would be created to build another bomb.

It took both weapons to get them to surrender, and a direct command from the emperor himself. Even so, there was a small revolt against the emperor and his command to surrender, something inconceivable in their society. Thus it is clear that the weapons had to be used to full horror to bring the war to an end, because the Japanese military was willing to die fighting and not even the Emporer was going to stop them. When the revolt was crushed, Admiral Onishi - the coup leader - committed ritual suicide.