I can't recall now an instance of "bueno" not being "good" and "bien" not being "well". Please, could you be more specific?.
"Bien" is "well", an adverb. "Bueno", "Buena" mean "good", an adjective. Examples: I feel well: Me siento bien Behave well!: ¡Pórtate bien! This meal is good!: ¡Esta comida está buena! (or "rica"). Notice we use "buena" so that the adjective is in concordance with the gender of the noun (comida) He is a good man: Él es un buen hombre (o "Él es un hombre bueno"). Notice that we don't say "Él es un bueno hombre" Hope this helps. Feel free to ask, and enjoy learning Spanish. Regards DG