Well, I recommend saving files as XML. When you write a document in MS Word, go Save As -> Other Formats -> Choose XML here.
You will be still able to open the document in MS Word and it will be easy to edit XML with PHP DOM or SimpleXML.
To add some text at the bottom, you just need to add a new w:p element to the XML body:
<w:p w:rsidR="00CF175F" w:rsidRDefault="00CF175F">
<w:r>
<w:t>New text to be added</w:t>
</w:r>
</w:p>
W is a namespace. For Word 2007+ it is:
http://schemas.openxmlformats.org/wordprocessingml/2006/main
In the older XML format there are different namespaces so you will have to look at MS web pages to find which one is correct.