Welcome in the forum, Magnus!
A PSoC runs with 1.8 to 5.0V. Telling Creator beforehand which voltage you will run at is used for trimming the clocks and calculating ADC conversions to voltages. As a general rule: VDDA must be the highest voltage and no input signal should exceed it. So you may program and supply your prototype kit with 5V from the snap-off programmer, you also may run it (after successful programming) at a 3.3V supply.