Note the disk number that corresponds to your USB drive, it should be obvious going by size.
select disk X where X is the number from above
select disk X
select partition 0
select partition 1
create partition primary
Exit Command Prompt (type exit or just close the window)
In Windows, go to Computer and try to open the disk. It will ask you to format it.
Format it with the default settings and give it a name if you want.
It should now a single, unified partitioned drive.
While trying to setup a new system with Windows Vista to use as my media center I ran into a strange problem. It would create thumbnails and show the video length for all videos, unless they were on the my USB drive.