You will have to compile it for the Intel chip using a Chip-specific compiler to generate code to run on the Intel chip.
You will also have to compile it for the Motorola chip using a Chip-specific compiler to generate code to run on the Motorola chip.

Thus you will need two separate compilers, and end up with two separate executables - one will run on the Intel chip only; the other will run on the Motorola chip only

You could use conditional-compilation to decide between the two; eg,

#if defined INTEL
// Intel-specific definitions
#elif defined MOTOROLA
// Motorola-specific definitions
#else
#error Unsupported chip!
#endif

It always pays to "encapsulate" your compiler-dependencies like this.