[Brian]

Happy to help!

Do the following:
File Menu -> Template Chooser...
Press "New Template" button in the template chooser.
Inspectors -> Canvas -> Size
Switch "Ruler Units" pop-up to cm.
File -> Save with whatever name you'd prefer.
(It should pick ~/Library/Application Support/OmniGraffle Pro/Templates by default.)

Just return to the template chooser, select the one you just created, and press the "Make Default" button. From now on, all your new documents will use centimeters instead of inches.