I've never had a problem with my vehicle at a parking lot on the north side of Q but I've never parked a motorcycle either.  Chain it to a tree?  Atikokan is a small town with year round residents so it has everything one might need but since you will be renting a canoe anyway you can leave your bike at the outfitter I assume.  I would pick a date and get a permit and hook up with an outfitter and rent your gear too.  What you save in gas you would spend in rentals.  Sounds like fun though.