Thank you. Distinguishing the uses of the simple present is something that I find particularly difficult. I would have thought that emphasising ешь would result in "Are you eatingthe apples?" ('as opposed to storing or selling them'). In English, emphasising the word implies that that is what you are querying - so emphasising "apple" makes it clear that you are asking about which fruit, emphasising "eating" emphasises that you a querying what action is being taken with the apples. I had assumed that emphasis had the same effect in Russian.
есть in the infinitive. For example, Я хочу есть = I want to eat (i.e. I am hungry)
By coincidence, it is the same as "to be" in the 3rd person singular (which is the only present tense form in use). Then again, the German words ist ("is") and isst ("eats") are also similar. But yeah, in the past these two есть had a different "е" sound :)
In this case, intonation. If you are wondering whether or not a person eats apples at all—it makes sense to emphasize ешь, i.e. there will be an abrupt peak of pitch on the word, and then the intonation falls.
If you are not sure what the person is doing at the moment (eating apples or what), яблоки will be slightly emphasized.