Hm, do we use "ja" here to refer to I because it's happening in the present? In other sentences we use "mnie" and I'm trying to figure out the difference.
Not with the tenses, it's still the beginning of the tree, we'll be only dealing with Present Tense for quite some time.
"jedzą" is 3rd person plural (they eat/are eating), and "jemy" is 1st person plural (we eat/are eating). Every grammatical person has a separate form of the verb.
I agree. I'm sure the plain "Jemy jablka" sounds better Polish. Over here, even in English, the simple "We are eating apples" would be the more usual or colloquial phrase . "She and I are eating apples "would be a rather rare expression (and "I and she are eating apples" would sound horrible!)