Last year we worked with Quetico North outfitters, right on Hwy 2, just east of Atikokan.  We did a north-to-south traverse through the Park.  It was a bit of a hassle getting it set up, but once on the water, it was wonderful.  Here's how we did it:

1. Before the trip we arranged with Canadian Border Outfitters on Moose lake, to allow us to park a truck and canoe trailer in their parking lot, and we arranged for a tow with them from Prairie Portage to CBO for the end of our trip. 
2. We had a friend drive us and all our gear to Fort Frances.  We met a driver (and co-owner)  from Quetico North Outfitters at a parking lot in Fort Frances.  We loaded our canoes and gear onto her van and she drove us directly to the EP Stanton Bay on Pickerel Lake. Very nice lady (can't remember her name!)  She had our permits ready for us.
3. We paddled through the Park, ending at Prairie Portage, got our tow to CBO, loaded up our truck, and drove home.

It was one of our best trips.

Hope some of this helps.

prouboy