I don't know if there's Série D and qualification through the state championships in Football Manager, but (in real life) the top two divisions have the 20 clubs playing each other twice (like in Europe), with 4 being relegated and other 4 promoted. the third and fourth division are also played by 20 teams, but they are regionalized with a series of group stages. qualification to the 4th division (Série D) happens through the state championships that take place from January to April, so if you're relegated from the 3rd division you're not guaranteed a league place in the following year. if you're a minor club, you should need to qualify to Copa do Brasil through the state championships too (in real life the top clubs qualify automatically through the CBF Ranking, so usually if a big team wins the state c'ship, a minor one will probably "inherit" his place)
you can grab a qualification to Libertadores through the top 4 spots in the first division or by winning the Copa do Brasil (or being the champion of the Libertadores), but if you're playing the Libertadores you can't play the Copa do Brasil. if you place between 5th and 12th you qualify to the Copa Sudmericana (which, if you win, qualifies to the Libertadores, but again, if you're in the Libertadores you can't play the Copa Sudamericana).
that means you'll either play the State C'ship, Brasileirão and Libertadores (2 ways to qualify for the next Libertadores) or State C'ship, Copa do Brasil, Brasileirão and Sudamericana (3 ways to qualify).