You will definitely want two sensors for each axis; total 4 prox sensors. Otherwise, you will be using "magic" to make stuff work, and that never ends well! I haven't worked with the capsense, but looking at the component in the topdesign.cysch, it seems like you can have 4 proximity sensors with x-sensor elements for each one? Since the x-axis versus y-axis is most likely software processing, the issue is most likely in your code for getting the capsense to work for 4 different proximity sensors :/
This needs to be implemented in the software. To begin with configure the proximity widget with 4 sensors so that all the parameters will be same for all the sensors.
Now to prevent both x axis and y axis to be triggered at the same time you need to handle this in the software.
For example if you move your hand across the board from right to left and due to this the Sensor on the top and right get some raw counts.
You need to see which sensor has more coupling and then disable the other sensor. If Top sensor has more coupling disable the right sensor.
So now only top to bottom gesture will be scanned and do the same for the other axis as well.