The MBR3 kits have an onboard kitprog that does the conversion from I2C to USB. In case you are using a custom board, you can use any I2C to USB converters or a Miniprog for connection.
There is an option to "Select Target Device" in EZ-Click. Make sure that the MBR device is connected to the computer and it will show up in the available ports as shown in the figure.
Do let us know if the connection is successful.
I was looking more on a hardware solution. I have a cy8cmbr3110 on a custom board and access to the I2C pins. Can I use an CY8CKIT-005 MiniProg4 to connect?