If you say that you like something or someone well enough, you mean that you quite like them or find them reasonably acceptable. Nancy liked it well enough, but complained about the color.

Do we say good enough or well enough?

Well, we do say "good enough", but in different contexts. We can say that we know (that) something is good enough. (Here "good" is an adjective.

Is everything is well grammatically correct?

“All is well” is OK. In your second example, the word “everything” should be written as one word, and the sentence itself sounds awkward. You could say this, for example: “Everything is going well.”