"Well" is an adverb. It basically change the meaning of a verb. Take a look at: "well done!", "he works well".
"Good" is an adjective, and its function is to give qualities to a noun. "She's good at maths" is an example.
I think that "I hope that you are good" fits well. "I hope that you are doing well" could be another instance. I hope that these tips help you.