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Napoleon made the Prophet into something of a role model, seeing himself as a new conqueror and legislator walking in Muhammad’s footsteps. During the opening stages of his campaign he relentlessly asserted himself as a defender of Islam and Egyptian people to bolster his legitimacy. He dressed in Egyptian costume, funded and celebrated the birth of prophet Muhammad, and Giving this missive immediately after his successful campaign:

...Egyptians, some will say that I have come to destroy your religion. This is a lie, do not believe it! Tell them that I have come to restore your rights and to punish the usurpers, that I respect, more than do the Mamluks, God, his prophet Muhammad and the glorious Quran ... Qadi, shaykh, shorbagi, tell the people that we are true Muslims. Are we not the one who has destroyed the Pope who preached war against Muslims? Did we not destroy the Knights of Malta, because these fanatics believed that God wanted them to make war against the Muslims?

Of course, this was all done to legitimate his cause. Islam was less important to him, of course, than legitimacy. Without legitimacy, the French could not hope to hold Egypt in the long run. He left instructions to French administrators in Egypt, explaining among other things that "One must take great care to persuade the Muslims that we love the Quran and that we venerate the prophet. One thoughtless word or action can destroy the work of many years.". However, Napoleon's admiration to Muhammad was probably genuine. During his exile on Saint Helena, Napoleon rote his memoirs, including the description of his Egyptian campaign. It is here we can see his views on Muhammad as conqueror and legislator. he wrote:

Arabia was idolatrous when Muhammad, seven centuries after Jesus Christ, introduced the cult of the God of Abraham, Ishmael, Moses and Jesus Christ. The Arians and other sects that had troubled the tranquility of the Orient had raised questions concerning the nature of the Father, the Son and the Holy Spirit. Muhammad declared that there was one unique God who had neither father nor son, that the trinity implied idolatry. He wrote on the frontispiece of the Quran: "There is no other god than God".

He addressed savage, poor peoples, who lacked everything and were very ignorant; had he spoken to their spirit, they would not have listened to him. In the midst of abundance in Greece, the spiritual pleasures of contemplation were a necessity, but in the midst of the deserts, where the Arab ceaselessly sighed for a spring of water, for the shade of a palm where he could take refuge from the rays of the burning tropical sun, it was necessary to promise to the chosen, as a reward, inexhaustible rivers of milk, sweet-smelling woods where they could relax in eternal shade, in the arms of divine houris with white skin and black eyes. The Bedouins were impassioned by the promise of such an enchanting abode; they exposed themselves to every danger to reach it; they became heroes.

Muhammad was a prince, he rallied his compatriots around him. In a few years, his Muslims conquered half the world. They plucked more souls from the false gods, knocked down more idols, razed more pagan temples in fifteen years, than the followers of Moses and Jesus Christ did in fifteen centuries. Muhammad was a great man. He would indeed have been a god, if the revolution that he had performed had not been prepared by the circumstances

Bonaparte’s Muhammad is a model statesman and conqueror, he knows how to motivate his troops and, as a result, was a far more successful conqueror than was Napoleon. Of course, Napoleon believed that Muhammad promised virgins in heaven for his troops, but it was in order to motivate them, and he was right to do so - his military successes proved it. He also decried the sanguinary doctrinal wars of early Christianity, with squabbles over the nature of the Father, the Son, and the Holy Spirit, and Muhammad's preaching cleared that. He even ready to excuse, even to praise polygamy. Why did Muhammad allow polygamy? First, explains Napoleon, it had always been a common practice in the Orient, Muhammad actually reduced it by allowing each man a maximum of four wives. Moreover, he believed that polygamy was a mean to combat racism:

Asia and Africa are inhabited by men of many colors: polygamy is the only efficient means of mixing them so that whites do not persecute the blacks, or blacks the whites. Polygamy has them born from the same mother or the same father; the black and the white, since they are brothers, sit together at the same table and see each other. Hence in the Orient no color pretends to be superior to another. But, to accomplish this, Muhammad thought that four wives were sufficient ... When we will wish, in our colonies, to give liberty to the blacks and to destroy color prejudice, the legislator will authorize polygamy

He also admired medieval Arabic sciences, and he believed Muhammad played a part in cultivating it. He contrasted urban Middle Eastern traditions of civilization with the traditions of the pastoral nomads of the Asian steppe and deserts, who, he said, constantly overthrew settled empires. The former were "enemies of the sciences and the arts," he said, "but this reproach cannot be launched at the Arabs, or at Muhammad". He continued "...Chemistry, distillation, sundials, clocks, our contemporary numerals, are all inventions of the Arabs. Nothing is more elegant than their moral tales, their poetry is full of warmth. Muhammad commended above all the erudite and men who gave themselves to a life of meditation and who cultivated belles lettres.”

So in conclusion, he did admire Muhammad, but it was his ideal Muhammad heavily influenced by his views and contemporary orientalism at the time. Napoleon’s Muhammad is a conqueror and lawgiver, persuasive and charismatic, basically resembles Napoleon himself, but a Napoleon who was more successful, and certainly never exiled to Saint Helena

Sources:

Napoleon's Egypt, Invading the Middle East by Juan Cole

European Accounts of Muhammad’s Life by John Tolan