CKCHONG,
Thanks for starting this thread. I have the same question. I am concerned if I bring the cover with me and make a mistake, it will zoom to the surface and be lost. But if I make a mistake the other way, I could scratch the dome.
I have been following RickM's advice so far and leaving it in the boat but making certain to hand it dome away from the boat..and having them do the same to me. So far so good, but my experience with SLR u/w is quite limited.
So far, I have been doing resort dives, not liveaboards. So I assume everything in the boat gets salt water on it, including the dome cover. So it gets a good rinse and dry when back at the resort.