3.3V and GND points are clearly marked on PCB (3.3V is located on the pin header above the pin 1, while there are multiple GND points). You can use the external 5V power supply if you connect the ground of the power supply to the GND of the PoKeys device.
The device already features built-in pull-up resistors, but on some pins, these are too weak to drive some of the stepper drivers. There is no problem in connecting pull-up resistors to 3.3V. The power supply is capable of handling the increased current demand (7mA per one pull-up resistor).