Glossary Item Box
These controls select which document will receive the links, what it will be called when completed, and to where the links go (the target file and its link map). In all cases, a Browse button is provided which will display the normal Windows file open Dialog to allow the user to select the file.
If the document is a standard with its own internal links (bookmarks) and was NOT linked when produced by 1st Word the Link-to-Self button can be used to generate internal links with this tool after the fact. Again, the normal style settings will be followed to determine where linking should occur.
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File to Process
The MS Word document which will have links added to it. Often a document the deployment user has created, which follows the normal 1st Word style sheet conventions so that linking will occur in the proper places. It is also possible for stewards to link a standards document in this way. In the case of guidance documents (users guides, example use fragments, code samples, etc.) that are not produced by 1st Word, this can be quite useful. 
File, New Name
The name of the final document is placed here. Note that you need to think about what the document will be called if any other document will in turn link to it. You can not change the name of an MS Word document once other documents link to it without losing those links. 
Link Map File
The link set to be used, an XML document which contains a listing of all the links in the target file that may have hyperlinks pointing to them. You can edit this list if the need arises in any XML editor. Once the file is selected, the name of the target files (the original MS Word document to which these links refer) will be filled in from the XML data. 
Target File (file to link to)
The target file (the file to which the link points). If you have selected the link set file, then it will be filled in for you. Otherwise, select the MS Word document where the links will resolve to.