Here is a way to do it very smooth, although not terribly useful in your case.
https://dl.dropboxusercontent.com/u/542 ... /pipe.capx
For your idea just break it down into smaller problems.
* For any given pipe section you need a way to find connected pipes. My capx did it by storing the uids, but you'll probably want to do it with an overlap check since you'll be adding sections when the game is running.
*After that the filling is much easier. You can do a method like I did or just make an animation for each section of the pipe filling from either direction. Then starting with some pipe, set it to fill. When it's full start filling the connected section.