Unlike alright and all right, altogether and all together are both legitimate usages with entirely different meanings. Their differences are best illustrated in this quote from the movie Airplane!
Striker: “Its an entirely different kind of flying, altogether.”
All Together: “Its a entirely different kind of flying.”
In Striker’s statement, altogether means completely or utterly (and truthfully, it’s a bit redundant in the sentence–entirely fulfills the same purpose).
The other characters mishear Striker, thinking he is asking them to repeat his statement collectively, as a group. Of course, in this example, the misunderstanding was exactly what the writers intended.
It’s just one of many examples of how what you hear and what you see on the written page can be very different things. Make sure you’re careful to write what you mean, not necessarily what you hear. Otherwise, your words can take on an altogether different meaning.