To create a "Prep by Amazon" shipment, please mark it as such in the "Plan Shipment" window, per below:
When you select to plan an "Amazon prep" shipment in Nineyard, it will set it to have Amazon perform all the prep work that is needed for the items in your shipment. We do not have a way of separating it to only do some of the prep, and not all, i.e., labeling and not bubble-wrapping.