Leave the books and magazines as they are.

Literal

Books [and-や] magazines [topic-は] as-they-are [adverbial-に] do-[prepare-ておく]-[gentle-imperative-なさい].

Several features. や joins nouns non-exhaustively ('books and magazines and whatnot'). そのまま ('as it is, unchanged') + に + する = 'leave as is, don't change.' ~ておく is the preparatory auxiliary ('do in advance / leave in place'). The combined そのままにしておく is a set pattern meaning 'leave untouched, leave as is.'