はいる means "to enter" (as in entering a building, or a bathtub)
You ask about いる, but actually, the verb you're looking for is いれる. It means "to put in" (as in putting something in a box).
They use the same kanji because either way, something goes in something else. はいる is intransitive, meaning it cannot take a direct object (the thing entered is followed by に, not を). いれる is transitive, since it does take a direct object.
You can tell them apart in writing because はいる is written 入る and いれる is written 入れる.