I was having problems finding any way to view all USB Flash drive partitions under windows x64, so I considered the issue and came up with a suitable workaround.
This method gives you a boot sector partition at the beginning of the stick (100MB or so, this is the MBR, we don't need to touch that) a second partition which will be bootable using DOS4USB (or your preferred method of creating a bootable USB drive) and a third partition which you can format as whatever file system you prefer and use as you would a typical USB stick.
The issue with Windows and USB flash drive partitions is that windows will only see the first Primary partition and assign a drive letter to it, so if we make the first partition a logical partition and the second partition *the* primary partition then Windows will simply ignore the first partition and assign a drive letter to partition 2.
The first partition is still visible outside of windows (it's still bootable, and is still visible under Linux / Mac)
The primary benefit to this is that your boot partition is protected against changes and fragmentation within windows. DOS4USB can't boot ISO's which are fragmented and this occurs if you modify the contents of the USB stick a lot.
EASEUS Partition Master 8.0.1 Home Edition (Freeware) - http://www.partition-tool.com/download.htm
USB4DOS (Freeware) - http://www.pendrivelinux.com/yumi-multiboot-usb-creator/ (Now YUMI, I used an old copy of USB4DOS but this should work the same)
Step 1: erase your USB drive, and configure using USB4DOS / YUMI (There are plenty of resources available to help you achieve this)
Test the USB stick and make sure it's bootable, and the bootable tools you need load.
Step 2: Load EASEUS Partition Master 8.0.1 Home Edition, resize partition 1 (the FAT32 partition, not the small MBR partition at the beginning of the drive)
Step 3: Create a new partition in the unallocated space and format to your preferred file system.
Step 4: Right click partition 1 and click Change drive letter, set it to None.
Step 5: Right click partition 1 and click convert to Logical.
Step 6: Right click partition 2 and click convert to Primary.
Step 7: Right click Partition 2 and click Change drive letter.
Don't forget to apply the changes!
Now under My computer you should see the large empty partition (Partition 2), try booting from the USB stick again.
if you need to make changes to the content of partition 1, simply reverse steps 4 through 7 make the changes and then apply steps 4 through 7 again.
Currently this is the best way I've found to achieve a bootable multi partitioned USB stick under Windows x64.