Just got back from another trip to the Island and I did the crossing to and from Tobermory again. The crossing itself isn't too bad if you check the weather. If coming from South Bay Mouth stay close to the Fitzwilliam Island shore in case of weather change. I always camp on the back of Yeo Island (2 spots: Yeo Spit or the Knob). Check the wind forecast to see what campsite to choose.
Hit the crosssing to Cove Island early and with high power. Get across this stretch of water quickly but watchout for the ferry (check ferry times ahead although, even in fog, you will hear it). If crossing ferry route in fog wait for it to pass before making your run. There are other large boats that use this route so have magnetic markers on your paddle and a fog horn handy.
This stretch of water intimidates even the most seasoned paddlers and rightly so. Ensure that you have all safety equipment including flares. Really keep an eye on the weather.
If coming from Tobermory all of the same rules apply and I usually camp on the east or west sides of Fitzwilliam for the night before heading north.
I've probaby crossed this stretch more than anyone else in a kayak so be careful. Although everything might go fine on a nice day this piece of water is very dangerous and has claimed the life of many an experienced sailor over the years. Hit the water hard and get the hell across...do not dawdle! Your stomach will have butterflies in the rough stuff!!!!

If the weather is clear you can change course to Flowerpot Island midway and this negates crossing the ferry course. If you have any more specific questions about the crossing please reply and I will get back to you.