There is a reason for this confusion. Caste in India has been a dynamic phenomenon and Manu's four classes with Brahmins at the top of the heap was more wishful thinking than an accurate depiction of the society he lived in. The division of society into four castes was a generalization that rarely held in practice. What is true about Indian society, even today, is that there are numerous geographically diversified but endogamous groups. The usual terminology for them is jati or subcaste.
At different periods of Indian history, different jatis have held power. The idea of learned people being at the top of society was one of Manu's myths. First, Brahmins have been at the top of the caste heirarchy "only" for the past seven hundred years of so in the North and less than three hundred years in the South. Second, Brahmins often were eager recepients of land (as in the Chola dynasty), and hereditary landowners often claim to be Brahmins (as in Bihar and U.P.). Yet, according to Manu's heirarchy, they would then be moving between first and third in the caste heirarchy ... The explanation is that the "firsts" and "thirds" were Manu's imagination. In reality, a jati moved up or down or the basis of its members' aspirations.
During the Chola reign in Tamil Nadu when the navy held sway as far east as Indonesia and the army as far as north as Orissa, money was sorely needed to keep up the military. Trade was also facilitated by the extent of the empire. The jatis involved in trade and commerce subsequently became the next most powerful (the royal family ofcourse was the most powerful). The Hindu stricture against crossing the ocean represents an (unsuccessful) attempt around this time by the priests to limit the power of the tradesmen.
It was only with the decline of Hindu military power with the advent of the Turks and the British that Brahmins moved to the top of the heap. They could offer themselves as intermediaries between the new rulers (whose religion and inclination developed a heirarchy distinct from Hindu caste) and their countrymen because of their education and because they had always performed this role for Hindu rulers. Since the Moghuls never really ruled the South (the Vijaynagar empire did), the structure never really changed in Andhra. To this day, the rulers and merchantile jatis dominate there.
Another way that jatis could move up in the heirarchy was by simply dropping off their old occupation and starting another. Note again that this option was rarely available to individuals -- they would have to form a jati first. Thus, for example, you have several jatis in Andhra that have traditionally been involved in trade but continue to follow Brahmanic rituals at home. Their family legends talk about a Brahmin group that decided to go into commerce -- because the commercial jatis were more powerful! A jati could also move up in the heirarchy in periods when imperial power weakened by supporting the right candidates -- exactly the way an individual would rise.
The point is that the caste system provided social mobility -- except that mobility was restricted to the mobility of a relatively small endogamous group. Such jatis (from 200 to about 100,000 people) were formed all the time, as the population of India increased and as familial networks became farther and farther flung. The actual power of a jati rose and fell with the times. The aspirations of a jati also changed according to the fashion of the day.
The process still continues, but with a twist. Jatis have found that in democratic India, power lies in numbers. What we now see is an aggregation of jatis into nominal caste groupings when seeking power and government patronage. The major difference today is that individuals are also socially mobile. Yet, in most cases, the mobility of an individual is shared by his family. Groups of such upwardly mobile families then become an endogamous subgroup of their original subcaste(s), in effect forming a jati. The language is gone -- such socio-economic classes will not describe themselves as jatis but they are.
Manu's concept of a stratified four-layer society, now as then, does not hold true.
I have borrowed from two main sources: "History of India Part I", by Romila Thapar and "Caste and Capitalism in Colonial India" by David Rudner. Needless to say, all misrepresentations and mistakes are mine and mine alone.