It's usually cheapest to just hunt around at the Hong Kong ferry Terminal and see who has the best 2 day package including hotel. Booking a hotel by yourself will work out to be the most expensive, there are a number of 2 day/weekend package deal agents at the ferry terminal, and in my opinion, if you are looking for the cheapest possible deal, that will be it...
You won't be dissapointed, unless you're the type that wants to pay peanuts, and expects 5 star treatment.. You get what you pay for, but they'll have something pleasant available, I'm sure...