You answerred this yourself:
不舒服 = not well, as in feeling a bit sick; headache or something
舒服 = not sick (LOL); well; no problems; no headaches; no nothing
好 = 1. fine, as in "I'm fine, how about you?"
2. = good, as in "a good fellow".
3. = to get better; recover from being 不舒服
Stop thinking of 不舒服 as a negative! That will help.