If you prefer to do this manually, you can use diskpart from the Windows setup command line to copy the setup/installation files from the USB to the local drive and then use the local drive to both boot from and install to, bypassing the USB completely and preventing Windows from getting confused:
list disk
(and make note of the disk number to install Windows to)select disk=0
(where disk 0 is your destination drive, so be careful, all information on this drive will be removed)create partition primary size=xxx
(where xxx – is the size of new partition)select partition=1
active
format fs=ntfs quick
assign
exit
cd d:
xcopy d: c: /e /h /k
bootsect /nt60 c:
bootsect /nt60 c: /mbr