In Permute, you can stitch (or combine/merge) multiple files into one. For example, if you have two videos, you can merge them into one. There are 3 ways of doing so:
Merge All menu item
You can select File > Merge All to merge all files in the queue.Drag & drop
You can drag a conversion using your mouse onto another one to get them to merge.
Contextual menu
Right-click the conversion or click on the preview image to get a contextual menu with per-conversion options. You can merge various files there.