If you want to create manual templates with PTGui, you will have to extract snapshots of your sources.
Here how you can do it in both VideoStitch Studio and Vahana VR:
Extract sources in VideoStitch Studio:
To extract sources in VideoStitch Studio, go in the Edit menu then Extract sources (or Ctrl + Shift + E) to and choose your target directory
Extract sources in Vahana VR:
To extract sources in Vahana VR, click on the snapshot button available in the Sources tab
The snapshots are then stored in C:\Users\YourUserName\Vahana VR\Snapshots