The JTAG chain is configurable within Zynq SoC. Cascaded JTAG works with an empty device.
You must provide a soft core to connect external pins to Arm DAP if Independent JTAG mode is desired. Refer to Mode Pin Settings and JTAG and DAP Subsystem chapters in the Zynq reference manual for more information.
1. Open Hardware | CPU Options | JTAG.
2. Set JTAG prefixes as depicted for Cascaded JTAG.