You really can't do one without the other. If you enabled the eBay shipping and payment details, then the carriers and costs are submitted to the eBay checkout form.
From what ive seen so far, specifying the shipping costs and any carrier, including eBay's 'standard flat rate' nonspecific type carriers are ok, so long as you list something as a carrier/cost.
This isn't to say they won't change later on and force sellers to indicate the exact service actually being used to ship the item, but that doesn't appear to be the case for the current announcement they made on this issue.
