To answer your second question first, yes, Jefferson did know Lewis before the expedition. The Jefferson's and the Lewis's were quite close friends. Later on in life, when he was putting together his administration, Jefferson wrote to ask Lewis to become a secretary-aide because of Lewis' military experience, education in the various sciences, and passion for the country, to name just a few. This suggests that Jefferson had an expedition into the West already in mind, and had Lewis specifically in mind to lead such a venture. When the Louisiana Purchase was made, Jefferson immediately jumped to do just that.

Originally, he appointed Lewis as Captain of the expedition because, as Jefferson described Lewis, "It was impossible to find a character who to a complete science in botany, natural history, mineralogy & astronomy, joined the firmness of constitution & character, prudence, habits adapted to the woods & a familiarity with the Indian manners and character, requisite for this undertaking. All the latter qualifications Capt. Lewis has." Jefferson then set about providing him with further education in the subjects he would need, including further medical and navigational training. Jefferson even served as a teacher for some of these subjects.

Lewis, however, wanted a partner to go with him. So he got permission to ask his former commanding officer William Clark. Clark was also a military man, skilled woodsman, and fairly intelligent if not as book smart as Lewis. Clark obviously accepted Lewis' and Jefferson's proposal, and jumped up a whole rank so that both men would hold the same rank and power during the expedition. Both men worked well together and everyone, including Jefferson, knew it. They were honestly the best suited to the job because of their various strengths. Jefferson could have easily sent a separate botanist, surveyor/map maker, woodsman, etc. but these two men had enough experience and schooling in all the necessary subjects that it was not necessary to do so.

If you have any more questions or if anything is unclear, feel free to ask. I work at one of the Lewis & Clark museums/historic sites along the trail so this one of my favorite events in history.

the answer is yes. Thomas Jefferson's family and Meriweather Lewis' family were both wealthy Virginia planting families and they were close since before Thomas' birth. Thomas and Meriweather were childhood friends and when Jefferson became president he made sure that Meriweather Lewis was involved with him in some capacity. When it was decided that Lewis wuld lead the expedition west, Jefferson took Meriweather Lewis under his political wing. Lewis lived at the white house with him and "trained" under Jefferson. Lewis was given the power to pick his traveling companion/co leader and he picked his own close friend from the military, William Clark.

Source: Meriweather Lewis biography by Stephen Ambrose.