In the PERRLA Add-in, your Word documents are completely normal Word documents.
Since the PERRLA Add-in lives inside Word (and doesn't have a separate application), you can save and organize your papers wherever you want – just like any other Word document.
You can manage your papers however you'd like. There's no required folder, no special application needed to open them – just open them in Word as you normally would.
Note: If you move your paper to another computer, you can still use PERRLA with it. You'll just need to add the PERRLA Add-in to Word on that computer first.