Look in AC9 HELP file: Introduction to Office Standards > Tailoring ArchiCAD > The Project Template File
Have you already created PROFILE for AC9 according to your office/working Standards?
If no then Start AC9 with default options and create new file.
Create your own working interface(Tool Palettes, etc.)
Then set the options in Working Environment (options menu) as you wish to see and use them always when you start or create file. Save this all as profile (for example: Office Std AC9 Profile) & set your std profile as default.
Next if you have std "Attribute Settings"(Pens & Colors, Line Types, Fill Types, Composites, Materials, Zone Categories, Mark-up Styles) apply them with "Attribute Managernger".
If you have or need std "Display Options Combinations" then create them.
In Library Manager set Std Libs to be Load at app. start-up.
In Add-on manager load/unload add-ons that you wish or not to use.
Save File As Template