Cut off top

When making a two-bottle rocket, you'll cut one end off the bottle that will eventually be the front of the rocket. Kids naturally tend to cut off the bottom, keeping the cap end to make the front of their rocket more pointy. Their intuition is that a pointed front will make their rocket more aerodynamic.

For a supersonic jet that would be right - you would want the front pointy. But for these rockets a rounded front is actually better. Think of a submarine, or Boeing jet - the front is rounded, and the rear is pointed. So I recommend cutting off the cap end, as shown in the picture.

If you'd cut off the original bottom, then the you'll have the cap end at the tip of the rocket, with screws and a lip that would cause vortexes, and are poor aerodynamically.

Rockets that keep the original bottom are also more durable. When a rocket comes back down it flips over, and a pointed tip gets crushed into the body of the rocket.

The front end isn't perfectly rounded. You can use duct tape to round off the top, optionally with playdoh underneath.