Currently, ShipCenter only allows packing in eaches. That can cause trouble as the shipping users need to calculate the eaches manually. We've run into situations where packages are not distributed correctly because of errors in these calculations. This would be addressed if ShipCenter allowed you to pack in the Sales Line UoM instead.
Official response
This is actually available as of ShipCenter 1.3.0.0! There are a few configuration elements that are relevant here:
New Shipment Editor security: Allow Entering Quantity Before Adding To Package
Allow users to set the quantity and UofM before sending a line item to a package, instead of automatically assigning the full quantity
New Shipment Editor security: Can Pack Items In Non-Base UofM
Allow users to pack items in any allowed UofM for the given item
New Shipment Editor security: Default Packing Quantity
Specify whether the default packing quantity is 1 or the remaining quantity to pack
After upgrading ShipCenter to 1.3.0.0 or later and updating the above configuration, your users will be able to pack in eaches or cases as needed!