I've paddled the Maligne a few times, in both high and low water conditions.  It is very rocky so if low water, you may have to get out and walk the canoes a little over gravelly shallow areas.  September is generally lower water.  You should be able to do the entire river in one day.  There are campsites at the mouth in Sturgeon, a nice one at Tanner Rapids (north/west side), also a nice one at the end of the portage at Twin Falls (buggy mid-summer but probably just fine by September).  The portages are easily found and easy to do.