The KitProg stub on the CY8Ckit-059 board is a 5 volt only board. But, with an interesting trick mentioned by the Cypress user EvPa_264126, you can modify the KitProg stub to work at 3 volts, and safely program 3.3 volt units. These modifications are more or less permanent.
If you can’t register, or don’t wish to, the image that the user published is here (shown under the fair use act):
How It Works
All LED’s (Light Emitting Diodes) essentially are Zeners that emit light. They take the current going through them and convert most of it to light. During the process, they also regulate the voltage across the LED to 2 volts. So, 5 volts in on VDBUS (the USB standard voltage) minus 2 volts for the LED gives you 3 volts to power the VTARG (and the programming voltage for the PSOC output).
The Possible Issues
Most LED’s are limited to about 30 milliamps before they overheat. Especially the ones you solder onto the board like this. Do not attempt to power your target board from this 3 Volt supply unless the current drain is within the LED tolerances. You could end up with a dead LED and a dead target. Why? LED’s usually short out when they burn up. 5 Volts – 0 Volts = 5 Volts == dead target board if it is not 5 volt tolerant.