I've never hung a boat from by garage roof, but I keep all my sails and the like up there.

You could make a cradle forthe boat and then hoist it up into the rafters - Make sure you have a VERY good fail safe so the boat cannot fall down.

I would not store it on it's side for any length of time - this will do the beam bolts no good at all - they are designed to hold the hulls in compression, not shear !