Learn French: N'en mange pas trop. - Don't eat too much of it.

You are thinking of the rule for positive commands! In a positive command, we keep the 's' to make pronunciation easier (like Manges-en). But in a negative command, the pronoun en goes before the verb. Because they aren't attached, the verb goes back to the standard tu imperative form for -er verbs, which drops the 's': mange.

Why is en placed before the verb? Aren't pronouns supposed to attach to the end of commands?

In positive commands, yes, pronouns attach to the end with a hyphen. But negative commands (commands using ne ... pas) follow normal sentence word order. The pronoun goes right back to its usual spot immediately before the verb, giving us N'en mange pas.

What exactly is en replacing in this sentence?

The pronoun en replaces a noun introduced by de. If you were talking about chocolate, the full thought would be Ne mange pas trop de chocolat (Don't eat too much chocolate). The en stands in for de chocolat (of it), saving you from repeating the noun.