The USB Flash drive must be partitioned and formatted. Start with the following steps on MacOS.
It helps to only have the one USB Flash drive plugged into the computer when running this command
diskutil list
Replace the '<NAME>' with the volume name from above and the '<disk>' with the disk name noted above.
diskutil eraseDisk JHFS+ <NAME> <disk>
Next perform the following steps on Windows.
If Windows tells you that you need to format a disk, click the Cancel button
Finally follow the steps below to install the applications on each partition