Yes you can do a custom scan where you may select which areas of your pc OneCare will scan.
Just follow this simple step:
1. Under "Protection Plus", click Scan for viruses and spyware
2. A dialog box will appear and it will let you choose a scan
3. Select Custom Scan
4. Another dialog box will appear and now you can choose which area OneCare should scan.
I think when you choose the Complete Scan, OneCare will scan the whole system including the external and flash drives.