You can specify a Spacegroup or Resolution with the xds_runme.com script. 
    Just put them on the command line.  Like this:

  xds_runme.com P212121 3.0A /data/username/whatever/blah_1_

Or, after xds has run, you can repeat just the scaling step and change the space group that way with xds2mtz.com.  
Same syntax:

  cd processing/whatever/
  xds2mtz.com P212121 3.0A

As for merging data with pointless/aimless, all you need to do is this:
echo "choose spacegroup P212121" | pointless XDSIN XDS_ASCII.HKL hklout pointless.mtz | tee pointless.log
echo "resolution 2.5" | aimless hklin pointless.mtz hklout aimless.mtz | tee aimless.log
echo "nres 999" | truncate hklin aimless.mtz hklout merged.mtz | tee truncate.log

Modifying them, of course, to reflect the space group, resolution cutoff, and molecular weight you think are appropriate. 
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