Where did you find isolinux.exe? AFAIK it doesn't exists.
For booting from a USB HDD you need to partition a partition of the HDD in FAT16 or FAT32 and you need syslinux (for partitions formatted in FAT16 or FAT32) as bootloader instead of isolinux (for CDs)
Copy all the files which are inside the iso on it.
Download the last syslinux version: http://syslinux.zytor.com/
Extract /win32/syslinux.exe from it.
Open the command prompt (cmd.exe)
Drag and drop the syslinux.exe file to the command prompt.
syslinux -ma -d syslinux x: (replace x: with the drive letter for your USB HDD)
There is also a script in /tools/ubcd2usb that you can use. It is designed for USB thumb drives so I don't know if it works for USB HDD. The script does format your hard drive, so you loose anything that you have on the drive.
Search the forlum for syslinux and you will find a lot of posts.