Both can be translated as 'the bread' or 'bread'. The difference has to due with its grammatical case, the role the noun plays in the sentence.
Panis is the nominative singular, the subject of the sentence, the thing doing the action or being described (as it is here). It can also be the genitive singular, but the course currently does not use the genitive form panis.
Panem is the accusative singular, the direct object of the sentence, the thing the verb action is being done to.
Vir panem habet -> 'The man has the bread' or 'The man has bread'. The having is being done to the bread.
Panis bene olet -> 'The bread smells good'. The bread is the thing giving off a smell, the thing doing the action.