By 1860, the Manchu were in full flight to the Manchu homeland. Many of the Manchu and Qing officials were taken by surpise at the pent-up ferocity that was unleashed upon them in northern China, including Chinese Turkestan and Mongolia. At the root of it was the dual reasons of the humiliations that Manchus had placed over the centuries on non-Manchus, and the corruption that had become rampant in the Qing civil service. Some Western observers may have been tempted to believe that with so many of the career civil servants driven out of their posts, that the new regime would collapse into chaos - however, they would be forgetting the great number of talented Han, Hui, Mongolian, and others who had been candidates for civil service but denied due to being unable to find patronage or a big enough bribe. Therefore when the new dynasty (called Chuen, meaning Pure in Chinese) announced that the Middle Kingdom would return to a more fundamental Confucianism free from bribery and corruption (and with the number of executed or fled bureacrats, few disputed their ardor in reform), there were more than enough bright and well educationed non-Manchus free of the taint of the old regime to take their place.
Again, a naive observer from the West may have expected the northern rebellion and southern revolution to embrace and form a new China. However, the north was now dominated by fiercely traditional Confucians, whereas the south had already started a government which had more in common with the liberal nations of the Western World than their Confucian roots. The anti-Manchu reaction in the south had been milder, more gradual, but had been going on longer, and while there was no official discrimination against Manchus, the former administrators of China were by and large ignorant and disdainful of the new teachings of the West, and chose to return to the north, and thence Manchuria.
Both the north and the south claimed each others' territory initially, but the south was weary of war, and the north far from secure with Qing Manchuria at it's doorstep. The United States, France, and Britain were able to act as mediators to arrange an armistice between the two powers, with only a tepid agreement to begin talks in future on possible reunification of the two disparate parts of China.
Manchuria itself stayed loyal to the scions of the Qing dynasty, and refused to recognize the legitimacy of the Chuen dynasty. But essentially, Qing ruled over nothing more than Manchuria, and that at the sufferance of the Russians.