Welcome to Science Buddies, and thank you for your question. I assume you are performing the following experiment:http://www.sciencebuddies.org/science-f
I looked into this project you and your daughter are doing. The short answer is yes, you will likely skew results.
The key mechanism you are trying to observe through this experiment is "Thermohaline Circulation". By doing the "flip" technique, the different liquid solutions (i.e. salty vs. fresh, cool vs. warm) are allowed to mix gently via a small interface area, thereby controlling the mixing variables to the maximum extent. "Pouring" one solution into the other via a funnel will likely cause rapid turbulent mixing to occur such that it would become the dominate mechanism by which the two solutions attempt to reach equilibrium. Any observations made while this turbulent mechanical mixing is occurring would be inconclusive with respect to any mixing (or lack of it) caused by density or temperature differences.
I agree the flip technique is rather tricky, but important. Keep practicing and I’m sure you guys will get it. For the reasons stated above, keep in mind to fill both bottles to up to the brim so there is as little space between the liquids when you remove the index card. The better you do this, the more you are literally placing a body of liquid on top of another body of liquid with minimal mixing due to that placement occurring (one of the variables you are trying to control).
I hope this helps.
"As the circle of light increases, so does the circumference of darkness around it."
~ Albert Einstein