There are two things you can do here. One is to go to the "Monitoring and Reporting" node in the Server Management Console and click on Change Alert Notifications. You can then click on the Performance Counters tab and turn off Low Disk Space perf alerts.
The other solution is to load Start->Program->Administrative Tools->Health Monitor console. Expand "Small Business Server Alerts" tree node. Expand "Core Server Alerts" tree node. Right click on "Low Disk Space" Data Collector. Select properties Click on "Details" tab For the "Instance" field select Browse Select the specific volume you want to monitor Click OK on the browse dialog. Click OK on the Data Collector dialog. Right click the disk space node. Click copy. Right click the "Core Server Alerts" node and click paste. Do this so each specific drive will now have its own collector. Edit each of those new data collectors to reference the correct drive (aka instance). You can now close health monitor. If you go and load Change Alert Notifications, you will now see an entry for each collector you created.