Definitions in the labware library are already pre-loaded on the robot. If you made a custom labware definition via labware.create() you will need to load the definition as a part of your protocol. Read more about labware and our API here.
All labware in the labware library is already accessible in the Protocol Designer. When you click "Add Labware" while hovering over a slot in the deck you'll be presented with a list of labware to choose from.
At this time there is no way to add a custom labware definition to the Protocol Designer.