You will need "Power Cycle" mode and supply power from the miniprog3 to your board. Check the max supply current of the board vs miniprog3 capabilities. Leave XRes open.
I have same question but I'm using a CY8C45AXI-483, it has a XRES pin. I would like to know how to connect the miniprog3
Easiest in your case is: Using the 5-pin interface Vcc, GND, XRES, SWDClk, SWDIO.
Set Miniprog to "Reset mode" and set pwr supply to miniprog or external.