Hi lahrach,
The first thing for you to know is to use Xilinx's XPS (EDK). If you are not familiar with it follow some tutorial searching in google. If your doubts come from the bitstream format the document to read is the Virtex-5 Configuration Guide. Info in this way is a bit confusing, I'd tell you to follow the bitstream example in there and see what's the meaning of the commands there. When you learn that you can try to figure out your own bitstream commands. These commands can be sent through the Hwicap peripheral in XPS. You'll also have to check its drivers to know how it works (not that difficult).
Hope this helps you,
Regards