Each PDF file added to ArcSite must live in its own unique drawing within a project folder. There isn't a way to add two separate PDF files into a single drawing using the current ArcSite tooling.
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💡However, if you combine separate PDF files into one multi-page PDF, you can upload that into a single drawing.

Adobe has a free PDF combiner tool here. It may require signing up for a free Adobe account, but I think you can get unlimited use out of it without having to purchase an Adobe subscription. There are other tools online (and possibly apps) for combining PDFs. Example tool at https://combinepdf.com