Oooh, somebody who understands the power of quarantine!!
I'd do both honestly. Or rather, I would grab the inverts first, since you'll have to feed them for a good 80 days, and by that time the vertebrates will have done something to cause a small bloom of food for them. So grab your CUC and a pretty coral and start quarantining. Then when your wallet allows you to, grab your first fish and stick that in the quarantine system.
I think that it depends on what you're quarantining for. If you're mostly worried about ich/velvet, then yes, you could theroetically make the DT invert only as long as you didn't add any fish to the tank. Now, banded sea kraits (certified verts) probably wouldn't worry about ich/velvet, and are a nonissue when it comes to most disease.
BUT, if you're worried about pest algae, coral pests, or anything else, I would quarantine in the designed invertebrate quarantine tank. It's far easier to manage in a smaller system than in a larger system. Plus you can just, hydrogen peroxide and tear down everything if things go bazonkers in the QT as opposed to the DT.
