I was not looking at a chart and didn't realize what you were talking about. The south side of Mantoulin is open to the prevailing westerlies and you'd want a very protected harbor to ride out any storm. There aren't any. There are several fair weather harbors but nothing well protected.
Considering how fantastic the N Channel is, I wouldn't bother with the s. side.
The Benjamins, Croker, Fox, Baie Fine; all fantastic places. I could spend a month just poking around those places and be very happy.
I would come up from Killarney to Covered Portage Cove and west around to Baie Fin. Then hit Little Current on the way to the Benjamins, etc. Hit the places you missed on the way back.
There are places where you can tie to rocks in a hole big enough for only your boat. Very cool spots all around.