Daaf,
Sorry for the late response. You are correct that you can either use HSDC Pro to push in the rbf firmware or enable the JTAG port for this purpose and use it with Quartus tools. Load the firmware first via JTAG, then HSDC Pro will check the firmware ID on start up via the SPI access and you will not be required to load firmware again unless you switch devices which require a different firmware than already loaded.
If you look at the schematics from the TSW1400EVM product page you should be able to see which lines will enable the JTAG connector.
Ken.