If you have correctly identified the disease as velvet, you should not need to use Maracyn. What is the brand name of copper you are using?
Since this is a new tank, you'll need to closely monitor nitrite and ammonia. Be prepared to do water changes frequently to kep these as low as possible. If you have a foam block or filter media you can transfer from the diplay to seed the new tank, this will help greatly. (NOTE: do not move it back to the display once treatment is complete as it will be contaminated with copper.)
Unfortunately, most salties (myself included) learn the need for QT just like you did - the hard way.
It is a violation of federal law to use this product in a manner inconsistent with its labelling.