Hello,
Backup Exec System Recovery creates a separate recovery point for each volume it is protecting. In your situation, you will have two recovery points or recovery point sets. After you have converted each recovery point or recovery point set to virtual format (.VHD in this case), you will end up with two virtual disks.
One virtual disk will represent your C:\ drive, and the other will represent your D:\ drive. Add each virtual disk to the virutal machine you would like to run them on, starting with the virtual disk corresponding to your C:\ drive.
Let me know if you have any further questions.
Thanks.