Stratix III + JTAG on HSMC port

I am waiting for delivery of the Stratix III Dev board and am making a daughter board to connect to the HSMC ports. I use Altium with a JTAG that has a configurable software JTAG in addition to the hardware JTAG. I am connecting the software JTAG to I/O pins on the HSMC.

Do I have to connect the hardware JTAG to the JTAG Header, bypassing the "USB /MAXII Byteblaster" with the dip switches or, can I use the HSMC connector.

(From the table 2.7 in the Stratix Development Kit Reference Manual)

What I am asking is can you have "External USB Blaster" with Startix III target device AND HSMC port A.

The documentation suggests NO, is this the case?