What's the best way to create and edit a PDF where the source document is also a PDF?

Hi,
To be specific, we are in the process of upgrading our A/P processes and we have received a user manual from the company we contracted for the upgrade. I've been tasked with customizing this manual for my company's specific processes (this is with the permission).
What is the best course of action to accomplish this? I thought I should save a copy of the manual, and then modify each page as necessary. I will be adding and deleting text and graphics. I have never used Acrobat before, but consider myself a quick study.
Any suggestions wil be greatly appreciated.

When Acrobat saves to Word 97-2003 format, it actually writes a Rich Text Format file - the binary .DOC format used by Word is a closed standard. The .DOCX format is just XML, and neither export process cares if you have Office installed or not. In theory, OpenOffice can read both types of file; but there does tend to be some minor difference between how OO arranges things and how MS Word does it.
The critical thing is that if the PDF file has structure tags (i.e. it's accessible), Acrobat can flow the content properly in the exported file and can identify things as headers, quotes, lists, tables, etc. If not, it has to guess what the reading order is based on where things are on the page, and it will often get confused by intricate layouts, spanned columns, etc. There are of course some things (such as Word Art) which don't survive the trip to PDF and back, and will show as an image.

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