I would like to create a 64GB multiboot usb drive.I want the first partition to be a 32GB fat32 partition so that I can use it for accessing files from windows. (Windows only displays the first partition on a removable drive).I then want to put a couple (or more if possible) of linux distros on the later partitions.I assume I will need a small boot partition (ideally syslinux)... but it can't be the first partition.How would I best go about this setup?All the utilities I have looked on (linux and windows) for making multiboot USBs don't give options for having an extra partition at the start of the partition table.
Multiboot USB with extra first partition
partition;usb drive;live usb;bootable
I believe the tool you are looking for is YUMI.  I have almost the exact same setup you are referring to on a 64G USB drive.  You didn't specify if you wanted these to be Live distros or full installations, but here is my personal setup:64G USB flash drive formatted using whatever format YUMI specified (I forget, but I believe it's Fat32 -- but it doesn't really matter, since it just works out of the box).  From within YUMI, you can select multiple Linux ISOs, which it will give you the ability to Live Boot from whichever one you select at startup.One thing to note, however, is that if your USB drive is not currently in the format that YUMI prefers, it will need to reformat the drive accordingly, so make sure any important files are not currently stored on the drive before re-formatting it to instal your first Linux distro.YUMI automatically stores each of these distros in a directory on the root of this USB drive called multiboot, which contains everything related to YUMI and the stuff that is needed to run your Linux distros. You can use the rest of this USB drive to store whatever you want.Personally, I have win, osx, and nix folders containing important tools and portable apps, and these directories are on this same USB drive right alongside the multiboot directory.  If I boot into an OS normally and then insert this USB drive, all of my files are available to use.However, if I'm on a Windows machine, I have the ability to boot directly from this USB flash drive into the YUMI bootloader (which I believe is a customized form of GRUB), and it allows me to select from all of the live distros it has installed in the multiboot directory.  I think it even gives the option to boot Windows normally, or it may just be an exit option, which just reboots and then I can boot Windows normally from the internal drive.If you want to persistently-preserve files across reboots and run Linux like a full installation, I believe YUMI has the option to create a separate static partition on the drive, but it claims to be limited only to Ubuntu.  It may work with Debian as well, but I have never tried this method.  Then again, I could be getting this specific feature completely confused with a feature included in UNetbootin, which the last time I used, did not support all of the multi-boot options that YUMI supports.  In my personal opinion, YUMI is way better than UNetbootin.It should be known, however, that I did encounter a downside when using YUMI:At one point I had live versions of Backtrack, Knoppix, Crunchbang, and Linux Mint installed via YUMI.  A few months later, I wanted to load this USB in YUMI and remove Backtrack and replace it with Kali Linux, but YUMI informed me that they had upgraded their bootloader, and as a result, if I wished to install additional distros, I would have to reformat the drive and start over from scratch using their new bootloader, which was incompatible with the older distros I had previously installed that used their old bootloader.This would not be a huge deal, but it would be an annoyance to tar the contents of my normal files and move them off the USB and then re-install all of the other Live ISOs that I wished to keep via YUMI.  However, it would more than likely be a dealbreaker if you wanted to have a separate partition to store files across reboots (which like I said, I could simply be confusing with a feature of UNetbootin, as opposed to YUMI).All of that being said, from your specific question, I believe YUMI should adequately benefit the purpose of what you are looking to achieve.  It's a great tool that has served me well in the past.