The supports in V5 are already exported in the factory file, so just File > Save Factory File As.
If you want to make a minor edit to your part but keep the supports you already added in S3D, then you can use the new live reload feature in S3D V5. With that feature, the software will automatically reload the changes to your STL file, but it keeps all of the other information you had already added to that part in Simplify3D (position, rotation, custom support structures, process assignments, etc). You can go to Tools > Options > Models tab, and check the "Enable live reloading of modified 3D model files" option to make sure the feature is enabled. Then you just overwrite your original STL file with the modified version and you will see a prompt in the software to reload the part.