To just run your program, you can add an init job for it so that it runs when the system starts up. If you are trying to make it the only thing that runs on the box, then it is a little more complex.
A bootable system has 3 pieces:
1) Bootloader - after the platform firmware runs it starts the bootloader. Usually, you would use a standard bootloader like grub or grub2. The bootloader can have a menu to let you either boot your standard system or your test system.
2) Kernel - The kernel starts up and initializes drivers and then starts up a user space init program.
3) User space - Normally your user space is on disk, has shell, desktop and services and is mounted by a stock ramdisk image. In your case, if you just want to run one standalone program, you can do it all in the ramdisk. There are plenty of tutorials on the web on modifying it, like this one:
http://backreference.org/2010/07/04/...itramfs-files/
You would have to add your program, plus any libraries that it needs into the ramdisk image, and start it from the init script. For extra credit you can make it the init program so no script is needed, but I can't fit a proof of that in this margin.
