The "an apple" in "it is an apple" takes the article ein because the verb "to be" equates two things. In this sentence, both "it" and "apple" are nominative case. "It is an apple" = "Es ist ein Apfel."
The "an apple" in "it eats an apple" takes the article einen because the apple can receive the action "eat." In other words, "apple" is accusative case here and the article changes. "It is an apple" = "Es ist einen Apfel."
Tl;dr - ist and isst is pronounced the same way. If the object is masculine singular, the article attached to it should be able to let you know if the verb is ist or isst. If the object is feminine, neuter or plural, context is the only way to tell the difference.
Same word, same meaning. The difference is the case. For masculine nouns in nominative case it is "ein". For masculine nouns in accusative case it is "einen". Any follow up questions can probably be answered here: http://www.duolingo.com/comment/370405
There is probably info there that you don't need, but there are several links that should be helpful.
In Portuguese the verb "to be" is "intransitivo" which means that it does not need a complement/an object. I concluded that since the noun "Apfel" is not recieving the action of the verb (the verb is "intransitive"), we need to use the "basic form", not the "accusative". If I am right, we will never use the accusative with the verb "to be" (and also not with no other intransitive verb)