Origami is a stand-alone application that installs a plugin into Adobe Illustrator that helps the applications talk to each other. You need to run both Origami and Illustrator to use the Origami. Please see here if you need any help with Origami installation.
Edit the dieline and fold lines directly in Illustrator by giving the paths specific names. Then see the folding results in the Origami window. See the 3D Preview page for more details. You can read more about Illustrator interactions here.
Finally, when you are happy with the 3D shape you see, you can save it as an image or export it as a 3D file. See the Saving Results page for more details.
If you have question about using Origami, visit our tutorials page first to see if what you need is explained there.