rau,
The executable format for all uCLinux applications is FLT. There should be a bin2flt and/or elf2flt that will help you to produce the correct format.
Regarding your second question, this is really a Linux-specific question and I don't think you really want it to behave as you state. uCLinux will behave the same as any other Linux system, in this respect.
You
want a terminal! Initially, it makes sense to run your application via the command line, in the terminal. Once you've tested that it functions, there, you could start it via some sort of initialization script.
Best Regards and Good Luck!
- slacker