This is one of my most favorite areas of science. I hope you have as much fun with this as I have had over the years.
You have the right idea about making all your towers have the same base width and height. This will cause them all to present the same cross-section area to the wind flow.
It sounds like you have a pretty basic wind tunnel there. You will need to ensure you expose each of your tower samples to the same air flow. You will need to be certain that the speed of the air reaching the towers is always the same. And, actually, you should be able to present the air and different speeds so that you can best understand the importance of air speed on aerodynamic effects. This is usually done by varying the speed of the fan in the wind tunnel.
The important thing you will need to do is find a way to measure how much force the air flow is exerting on each of your test specimens. This is essential. It is the only way to measure aerodynamic efficiency. Here's why:
The force exerted by the wind on an object is a function of the velocity of the air to the second power, the cross-sectional area of the object presented to the wind and a "drag coefficient". It is the drag coefficient you want to determine. Here is a ScienceBuddies experiment that discusses a lot of the details. http://www.sciencebuddies.org/science-f ... ml#summary
This experiment is set up to perform in water, but all the principles apply to what you want to do in air.
Measuring force in a wind tunnel can be tricky. I don't know how large your tunnel is, or how large your models will be, nor how much air speed you can generate in your tunnel. But here's a concept on how to measure force.
You might be able to use a roller skate, or some other small platform with really free rolling wheels. Mount your tower samples on it. Attach one end of a spring scale to the roller skate and the other end to the wind tunnel. When the wind pushes on your tower sample, it will put force on the tower that can be measured with the scale. It will be important to do this experiment with only the roller skate so you can determine how much force the wind is causing on it, and then subtract that from the readings you get with you different samples.
Here at our local high school, they have a really nice wind tunnel that has electronic scales in it that can measure "drag", which is what you are interested, as well as "lift". Lift is what lifts an airplane wing. If the wind tunnel you have available is too basic to make the measurements you need, perhaps you could find one at a nearby school, or sometimes a science museum will have a wind tunnel you can use.
I hope this helps. If you need additional help, just ask.
Whatever you do, have fun with science!