"Do I have to mail the original documents to you after sending the copies by fax?"
You can use "Will I need to..?" if you want to sound a little more formal. The plural of "fax copy" is "fax copies".
"Alternately, I can submit the original documents when I arrive in the USA."
It just sounded like a broken thought when you started the sentence with "or". Would you consider writing the sentences as one question?
"Will I need to mail the original documents to you after sending the copies by fax, or can I submit the original documents when I arrive in the USA?"