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Once you have files assembled into a PDF file, you can rearrange them in several ways. Click the "Organize Pages" icon on the right toolbar. (Or, click Tools → Organize Pages.)
Here's a video tutorial of the process:
Adding Another File
If you forgot to add a file, you can still do so after having created the PDF file. Recognize, however, that if you have many additions, and you have already created a Table of Contents, there are many more steps involved and you may be better off simply creating a new Table of Contents page, and recompiling a new PDF file.
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