I haven't been up that way for a couple of years. I think there are a couple of sideroads off of hwy 6 once you get about 5 miles south of Tobermory. I don't know how
good or bad they are though.
Oh.. and as far as I know, bikes are allowed on the Glenora ferry.
Once you get to Owen Sound there are quite a few options. The 503 through the Haliburton Highlands is a beautiful but hilly ride.
How many miles a day are you planning on ?