Coincidentally I have that very same boat for some Vikings I have; at 1/50, it's understandably poppular with historical wargamers.
I still have to try waterlining myself, but when I do, I will use this method I have seen on several different blogs over the years:
Build the ship, and then temporarily fix it to a flat surface, with plenty of room to spare around it. Then attach a marker to a flat block in such a way that the very tip of the marker is at the exact level you want the waterline to be on your ship.
Then slide the block with the marker around the ship, taking care that the tip of the marker is always touching the ship. Go all around the hull, till you have a continuous line all around the ship.
Then cut the hull by whatever means you have available along the line. This can be a hacksaw, a jeweler's saw (for which you will need to pre-drill a hole, obviously) or even a powertool of choice, such as a jigsaw, or, if your have the luxury; a tablesaw (safety!).
After the cutting, fix a large surface of sanding paper to the table and sand the cut edges of the hull smooth.
The nice thing about this method is that you can afford to be less precise when cutting, because you can sand the hull perfectly flat later on...