I don't think a straight forward binary copy will work in most embedded system programming. Embedded systems usually have different architectures and different machine codes to a normal PC (assumed to be your dev environment).

You need a cross-compiler to compile the source code in your development environment (probably a PC), and then upload the binary to your embedded linux box.

Your development environment should have a cross-compiler, an emulator, a debugger, and an uplink to your embedded system. Pretty much like doing Playstation 2 programming.