Hi,
You install the Matrix manager within windows itself. The bit you see before windows is hard encoded into the firmware chip on the board and can not be modified without a flash.
The software side of it shouldn't acturly be required as far as the rebuild is concerned as it should be an automatic process. What it is is a monitoring tool that will tell you the harddrive state and how far along a rebuild is progressing for you. As Ben said in the inital response it should give you an indication to the machine state and if the harddrive is faulty or it's just a raid configuration issue which may resolve itself.
If you install it in winows it should become a bit clearer to where the fault lays.