binary configuration files - a simple question

You can create compressed POF files in two locations. Under Assignments, Device, Device & Pin Options, Configuration ... select the EPCS configuration device and select "Generate compressed bitstreams". After compilation you will get a POF file that is compressed when the Assembler runs. If you have a SOF and want to create a compressed POF, then you can do this under File, Convert Programming Files, select your configuration device, highlight the SOF Data and click on Add File, select the appropriate SOF. click and highlight the SOF that appears under the SOF Data, then click on Properties, check the Compression box when the GUI box appears and click Ok. This will create a compressed POF as well that you can use in the JIC flow you mention, which allows the EPCS device to be programmed over JTAG.