Main Window
After opening Permute, you are presented with this main window. To start, drag & drop file into the window, or onto the Dock icon; or use the Open dialog from File > Open… in the menu bar.
Queues
After dropping files into Permute, they are sorted by their kind into queues. In total, Permute recognizes 4 different queues:
For each queue, you can set a different preset using the popup button in the header view of the queue. Additionally, you can change the preset by using the per-conversion settings (see below).
When you are good to go, press the Start button which will kick off the conversions in the queue. The Start button will turn into Pause so that you can pause the conversions while they are running. You can stop indiviual conversions by pressing the X button and you can pause individual files by Option-clicking on the conversion's X button (holding down the Option button will turn the button into a || (pause) button).
Per-conversion Settings
By right-clicking the conversion or clicking on the preview image, you will get a menu that includes various tasks that can be performed with the conversion. Note that most of these are only available before the conversion starts.
History
In the bottom-right corner, you can find a button that toggles history. You can view your past conversions here.