In an ideal world, the template you pick will be exactly the one you need and your project will not require any customization; however, there are many things you can do to tailor the project template to match your specific needs.
When it comes to tailoring options, projects and templates are the same. However, you should exercise caution when making changes to projects sites as you could lose these should you decide to design sync the site with its parent template at a later date.
Remember, any changes you make to a live project can be saved as a template.
Template tailoring options include:
Modify Lists to Support Project Management Process
Setup and Modify Project Management Reports and Web Parts