quote:
but putting down water from buckets just causes a 'rapids' effect which destroys any boats that travel down it.
Nah, it's not the rapids. All boats in Minecraft are fitted with a timed explosive device which will self-destruct at a point in time when it can achieve the most annoyance.
To solve the rapids though, you just need to keep placing water with a bucket on the different moving squares until they go still.
Oh, and they all have to be the same height - needs a level surface; you can't have still multi-height water which is connected.