There's a number of flows for this. The easiest is to just tell SysGen to generate the bitstream and use iMPACT. This is simply a configuration option in the System Generator token. Also, you can generate hdl or an .ngc and you can continue through the rest of the ISE flow (or planahead flow if you're in 13.3). I suggest you read the sysgen getting started guide and the sysgen users guide