You can partition a transcend USB external disk drive into 2 partitions using gparted. Visit http://www.gparted.org to get the software.
Using gparted, the USB drive can have 2 partitions one ext4 for Linux and one NTFS for Windows. Using NTFS allows the backup of larger files to happen without intervention.
Had you used a FAT32 partition, the maximum file size that you could backup would have to be 4 GB or less. This helps overcome that limitation.