The suffix "be" attached to "cipő" is enough here. So you don't need to do anything special with the verb "esik". Altough for adding emphasis you can say: "A piros alma beleesik/beesik a cipőbe" I would prefer "beleesik" here, but "beesik" doesn't sound horribly wrong either.
Sometimes cipő means a pair of shoes and sometimes it means just one shoe. Is there a way you can tell which?
Usually you can guess it just from context. In most cases in this course it can be either one shoe or a pair. In this sentence it's definitely just one shoe, because you have only one apple falling into it.
If you want to make it explicit, you can say "egy pár cipő" for a pair and "egyetlen cipő" for a single one.