If you're doing it by phone, then I'm not sure I know how to do it. I believe by phone you have to enter the school code then they ask for department code which you can specify or not. I've never actually done it via phone though. I am certain that submitting request via the internet will let you specify graduate office vs department.
Doing it by the internet you do this:
You select which scores to send.
Select state (or province? I've never submitted to any country other than US schools).
Then you are offered a list of schools to pick from in that state. Pick your school
Then it has a text box where you can type in the department name (e.g. physics, math, etc). You then select the proper department from a list. On this page there is also a "skip" button.