With the ferries I've been on, it used to be that the crew would like you to use the centre-stand (if your bike had one). For the last couple of years, the same ferries, they want you to use the side-stand (annoying BMW riders no end). They then tie it down with a single strap over the saddle, hooked to deck ties either side, until the suspension is compressed some.
I have to say it looks more stable to me.
In the end, I do whatever the crew tells me. Then, in the event of any accident, it's their responsibility.