Capsense behind glass
Since the capacitance change will be much smaller due to the extra distance, you will need to set the sensing algorithm up accordingly for the new setup.  

You can get an idea of things by displaying the sense value for pressed/not pressed on the LCD with and without the glass.
Then you can tune the thresholds, averaging, filtering, etc (e.g. a longer integration period is better for confirming the smaller change, but makes the response time slower) I imagine Cypress should have an app note on doing all this, Microchip have a few decent ones too if they don't have much (how useful depends on how the Cypress peripherals function, though they are likely to be very similar)