Always a good move to try in the water first, several of my boats are very noisy unless sitting in the water. It loads the prop for one thing and doesnt let the motor overun, and also damps down the hull vibrations.
Doesnt mean to say you wont have to re-align the bits, but if you dont need to then it makes life a bit easier.
Usually I go for a double coupling straight off, as then you definately never have alignment probs (within reason!!) The SHG marine plastic couplins are good for accepting masses of misalignment, they are a bit rattly though in thyemselves.
Ashley