It really is that simple!
You can place the files anywhere on your site that you want to.
For example, you can upload the files directly to the root html
folder or you can create a directory specific to each affiliate program
if you want or you can create one directory specifically for cloaked
The choice is simply yours.
Just double click the file after you have purchased, to launch the software, and begin creating cloaking files.
There are simple instructions contained within the software.