Hi Grego,
If you build the NicheLite stack as provided by FreeScale with the sample web server task, and upload it to your board, you will have a board that has a simple console interface and a few commands, along with a webserver that has a basic flash filing system implemented.
If you want to do more, you will have to make changes to the stack as supplied, either by changing some of the compile time options (by changing #defined constants) to compile in extra functionality or by adding additional tasks to accomplish what you need.
When you build the NicheLite stack you will create a binary image that can be flashed to the beginning of the CFM flash and the board will run the stack on booting up. There is no bootloader, so if you want to write application level code, that needs to be written as a NicheLite task. With these lightweight stacks and OSes there often isn't a concept of a separate executable file. If the OS provides task switching then applications are written as tasks that co-operate with the stack/OS and other tasks by only running when they have something to do. Even more lightweight stacks often just have a superloop - a while loop in main() that calls all the task functions in turn.
If you upload another OS like MQX or uTasker then you will not be able to use NicheLite - that won't be a problem, because both of these (and others) provide a TCP/IP stack, ethernet and UART drivers, etc, etc. Other systems may also provide better examples that you can adapt to your requirements.
Cheers,
Paul.