Connect USB Cable, set 3 jumpers 1-2, 3-4, 5-6, click detect, see this in Diamond Programmer:

Change LP1K to HX1K manuall, select BIN file to load into HX1K FPGA Configuration RAM, click on program..

FPGA is configured and should live.

Programming the SPI Flash is as easy too, there are 2 jumpers to be changed and then proper SPI Part has to be selected:

When this succeeds, then FPGA will load itself from SPI Flash on power up on reset event. Creating multiboot images is a bit more complicated, but that has time to be explained in next updates.