"It is not good."
Isn't よく also used for meaning "often"? I could see this becomig confusing, or is it always very clear?
Yeah, try not to think of it as two separate words, like よく and ない, but rather all one conjugated word, よくない
いい comes from 良い/よい so when it is conjugated it reverts to よい, or in this case よくない.
so "よく" and "にい" did different things separately but "よくない" it makes 1 word?
Maybe not so much "one word" but I think if you call it a "set" you're on the right track. よく (yoku) in this sentence comes from the adjective よい(yoi) or いい (ii), meaning good. ない (nai) is word to negate something. よくない as a set means "not good". Unlike English adjectives, Japanese -i adjectives change forms to convey negation or the past tense. -i adjectives drop the final "i" and add "ku" + "nai" to form the negative version of the adjective.