”tabete iru” means "someone is eating". We use "verb + iru" to express present continuous tense. And "obento o tsukurimasu" is not correct. "obento wo tsukurrimasu" is correct. You can write this sentense "こうさかさんがたべているあいだに、おかあさんはおべんとうをつくります。"

'iru' is used as end-form and adnominal form (form to modify a noun).'aida＝during' is a noun.

When a verb ends with the て-form followed by いる, it means that the action is taking place. In the sentence you gave, it means that Kousaka is eating while her/his mom is making the obento. Hope I managed to say it clearly. ^^'