What does it mean if you're not smelling amoxicillin in your urine?

No worries: Amoxicillin and other penicillin like antibiotics are excreted via kidneys and can cause dark urine and sometimes smelly urine. Lack of smell dose not indicate inactivity of the medication and you should not be worried about it.

Maybe stuffy nose?: Most people don't smell their urine. You can find on the Internet lists of diseases which have characteristic odors ( Maple Syrup Urine Disease, etc.) There could be many other issues here to be explored. Make a virtual consult to discuss in much greater detail.