The thing to keep in mind is that windows event id that LEM is looking for for disk space alerts is set up at the operating system level, the default being at 10% free space remaining. To change the threshold you have to edit the registry.
In order to limit your alert from LEM to just the c: drives you should add a filter to the default template for servicewarning.eventinfo = *C:*
Might need to play with the syntax since I don't have a box to test with handy but that should get you close.
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