Saving a document with method Save(), GroupDocs.Watermark puts it in the same folder as the original file, rewriting original. If you need to save the document to any custom location, you’ll have to use Save(string) method or Save(Stream) of Watermarker class.
You can see examples of Save methods in one of these guides:
Save document to the same file or stream Save document to the specified location Save document to the specified stream...Signature Product Solution GroupDocs...