Hey, there's a couple of things you can do.
In order to choose the location of all temporary files for red gate products you can set the RGTEMP variable. This is described in full here
http://www.red-gate.com/supportcenter/C ... wledgebase
You can also turn on "compress temporary files" in the data compare options. There is a slight downside to this, in that you can't sort the results, but it will considerably reduce the disk usage.