I came across a similar problem to some posters regarding not being able to apply multiple page templates in Dreamweaver. It's a crazy omission by Macromedia/Adobe as if you have 300 pages you have to do each one separately.
I made the process a little easier by creating a keyboard shortcut (which doesn't exist by default). Follow this process in Dreamweaver:
1. Edit > Keyboard Shortcuts.
2. Duplicate set (Dreamweaver does not allow changing the standard set).
3. Choose new set.
4. In the commands window, click Modify > Templates > Apply Template to Page...
5. In the Press key field, choose the shortcut keys you would like to use (Dreamweaver will tell you if they conflict). I chose Ctrl+Shift+/
6. Click Add.
7. Click OK.
8. Try out your new Shortcut.
It saved a great deal of time for me and, until Adobe improve the issue, is one of the only options I've seen.