Canada work permit and U.S. Visa Waiver Program

Hello,

I am an Australian passport holder, and I am currently in Canada on business as a Business Visitor for a few weeks. I arrived via the U.S. and so I used the Visa Waiver Program (VWP) to transit through to Canada. The VWP website says that I must leave the U.S. as well as Canada and surrounding islands within 90 days.

The local subsidiary of my company would like me to stay on and work here for up to a year. They will sponsor a work permit for me (and I have to leave and re-enter Canada via the U.S. to activate this work permit, which is fine as this will be done within the 90 day VWP limit)

My question is, once I have the work permit in place and am staying in Canada for the year, what happens after the 90 day limit for the VWP runs out? Will I be allowed to return to Australia via the U.S. as a Canadian work permit holder? Even though I entered 'North America' using the VWP and their website explicitly states I must leave North America before the 90 days is up? Will I have to re-route my trip home via Europe or something at the end of my assignment?

Any help would be greatly appreciated.

Thank you very much,
Mal