While you should really make your question clearer in the post, I've done some work with scripting Excel so I know that asking for confirmation to save is controlled by the Application.DisplayAlerts property. If you set that to false, Excel (and Word) should save the file with default values.

Hopefully that will solve your problem. However, this isn't really a Perl problem. MSDN is quite handy for these types of queries, and you should probably use that instead. Familiarize yourself with the Word Object Model.

Good luck.