On reflection, perhaps that should have been "for the purpose of", rather than "in order to":
1. We learn how to use, for the purpose of Y, X.
In other words, I would take the phrase "to alter or emphasize what we say and do" as an adverbial phrase that modifies "use", not "learn".
(Which is why "To alter or emphasise..., we learn how to use..." isn't a paraphrase!)
All the best,
MrP