Translation:How do you buy this on the Internet?
The difference is rather small: "Comment tu fais (pour...)" is a very common phrasing that asks what process you go through to achieve something: it's typically something you'd ask when you want to know how to do it yourself. For instance, if someone did something incredible before your eyes and you just don't understand how they did it, you may exclaim "Mais comment t'as fait !?" hoping they explain how they did it.
"Comment tu achètes..." on the other hand, is more neutral and descriptive. It could even be used somewhat sarcastically, similar to English "How come you buy that on the internet?"
In any case, the difference is very subtle and probably too little for a non native speaker to worry about, although familiarizing yourself with this "comment faire" expression will definitely help sounding more fluent.
And one last thing: I would personally translate this sentence as "Comment on fait pour acheter ça sur internet ?" since it's most likely asking how to do it in general, rather than how you do it specifically.