There are different levels of 'applying templates'. A large number of decisions need to be made to determine whether each document requires any/all of the possible steps. The things I would consider while doing this task are:
1. Attach Template
2. Refresh styles from the template (update the style definitions to match the template style definitions). May include updating color palette and font theme settings.
3. Apply styles to content that had the non-preferred style applied. In this step you may also need to remove local formatting by pressing Ctrl-Q and Ctrl-Space.
4. Replace covers and initial pages with standardised template contents (cover, TOC, version control, acronyms list etc)
5. Add standardised heading structure if this has been defined for different document types.
6. Replace header/footers for all sections
7. Standardise page setups for all sections

As you can see from the steps listed above, attaching a template is not a minor undertaking. Many decisions will need to be made along the way. You should get a good look at the range of documents that you have to convert and sit down with your boss and decide on how far they want to go and how much flexibility you might have in making decisions on the fly. I can guarantee that the 'template' will not have provision for EVERY formatting decision you will encounter but if you follow the basic principles you can make big improvements in the state of the documents.

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Andrew Lockton
Chrysalis Design, Melbourne Australia