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With main drive I suppose you mean have windows installed on it? I don't really see the advantage of doing so (having the larger disk as backup makes more sense to me) but anyway, you can proceed like this:
- take out the 180 GB disk
- boot with the windows CD and install the OS on the 350 GB disk
- put the 180 GB disk back in and copy over any files to the 350GB disk, then reformat the 180 GB disk to take off windows.
- it doesn't matter which is slave or master
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