1) De manhã/de tarde/de noite= in the morning/in the afternoon/at night. You just know that.
Ex1) Eu gosto mais de ter aulas de tarde do que de manhã. => I like to take classes in the afternoon rather than morning.
2) Pela manhã/pela tarde/pela noite = in the morning/in the afternoon/by night. It yields the image that you, most probably (may be not) , could have done (or will do) it intermittently or throughout all time.
Ex2) Eu gosto muito de ir à praia e tomar o sol pela manhã. => I really like going to the beach and sunbathing in the morning.
3) À tarde/à noite=in the afternnon/ in the evening (at night, tonight). It yields the image that you, most probably (may be not), are "waiting" fot that time to arrive and that you are not inside that time yet.
"À manhã" does not exist because it developed to "amanhã"=tomorrow
Ex3) "À noite, vou acabar de ler este livro." => At night, I will finish reading this book.
4) Da manhã/da tarde/da noite=belonging to the morning time/afternnon time/(evening+night) time.
Ex4) Neste momento, são 5 horas da manhã. => At this point, it's 5 o'clock in the morning.
5) Na manhã/na tarde/na noite=inside the morning time/afternnon time/(evening+night) time of a certain day...
Ex5) O crime deu-se na manhã do dia 5. => The crime occurred on the morning of the 5th.