There are many different ways to store application object code and data on an embedded system. The method depends on the target architecture, and what it uses for storage. Storage can be conventional spinning media, various types of on-board or on-chip flash, removable flash, or even no on-board storage, requiring network shares or running completely out of a RAM disk. If the storage is on-chip or on-board, it may require the use of a tool such as a J-tag dongle to download the data to the board. Sometimes there are tools that can be used to write the data to on-board flash. Sometimes, simply writing the data to the appropriate place in the filesystem is sufficient.
There are also numerous ways to launch your application at boot time, and the best method depends on the application, its requirements, and the target architecture. The bootloader, if present, may play a role in controlling application launching.
In summary, tell us about the nature of your target, and we can probably give you useful advice. Without knowing more, there is no way to advise you.
Last edited by theNbomr; 09-21-2012 at 08:18 AM.