Using diskpart on Windows to partition a USB stick
Open an elevated command prompt.
<C:> diskpart DISKPART> list disk
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 list partition select partition 0 delete partition select partition 1 delete partition create partition primary exit
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.