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.
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.