Generating download.bit from commandline
The general form for automating impact downloading is:

setmode -bscan
setcable -p auto
identify
assignfile -p &lt;index&gt; -file &lt;some-file&gt;.bit
program -p &lt;index&gt;
quit


saved in a .cmd file with  and  replaced as necessary.  Then you would run impact in batch mode as

impact -batch &lt;some-file&gt;.cmd


Seems like for your case, you should put 'system.bit' in the cmd file so that impact will try to load from the correct file.  

If this doesn't solve your issue, please add some more details to clarify.