I know it's not a run of the mill home pc, my question is more or less to try to home in on how it might be configured.
There are countless official linux variants available... and that does not account for the unofficial spin-offs that are commonly built and slapped in routers, refrigerators, and security camera DVRs ... :s
I'll overfill you with info now... and maybe it will help you during your experimentations.
First and foremost. Most embedded systems do not utilise the harddrive like conventional computers... They will typically have an 'image' which consists of a tar.gz or similar archive that is copied to memory when the system starts. The majority of the operating system is held in memory, and the image or harddrive is only ever utilized to read larger assets that can't be stored in memory. The problem with this setup, is that almost any modification to the file system will be lost on reboot. If you can confirm this is not the case it will make your life a lot easier.
Next up is the update... and there is no way to know for sure without a bunch more investigation. If the update is simply a script that runs to apply a patch or update software on the machine then you can most likely get away by mounting your USB device to the same path the CD-ROM usually resides, or by simply creating a symlink to it. A symlink can make a folder appear in more than one location which will let your USB drive be mounted as normal, AND also appear mounted as a CD drive.
If the update reboots the computer or replaces the current OS... then this method is most likely out of the question unless you will be creating or manipulating the system to automatically mount the USB device as you want it... the issue with fresh installs is that you will not be able to control this behaviour at all...
So.. now for a little explanation on common directories in linux based systems.
/usr/local/bin/UpdateSystem (don't forget the leading / ... it can make all the difference of where the file actually is!)
I will not discuss mounting points, and harddrive mounting points... that gets messy.
Almost any 'bin' directory will hold 'binary' executable files which are responsible for anything from showing a directory listing to allowing ssh access. There will typically be one in the / which takes care of most if not all system programs, and another in /usr as you have found. The programs in /usr/bin and /usr/local/bin are commonly additional programs such as data logging applications, or perhaps the software running on your machine.
/media /mnt and /dev will be related to USB drives, CD-drives, Video Capture cards, etc.
/proc is going to contain a bunch of 'virtual' files that define and show the current state of the system such as the number of processors, the current clock and all sorts of fun goodies.
/var will normally contain files that change a lot such as logs.
/etc will be configuration files, but there will be another etc file in /usr as well on occasion depending on the setup.
The vast majority of all things linux can be altered and manipulated with text editors... the exception will be the actual binary files in /bin /usr/bin and /usr/local/bin .. This also means that simply going around and 'reading' a bunch of files will give you tons of info into the system. For example... looking at /proc/version may tell you what the linux system you have is based on as well as a file in /etc usually named a variety of things with the word 'release' in it.
So. dig around, read things, careful changing certain files and let us know what you find out!
