If you feed a .s file into gcc it will just assemble it.
IIRC if you use .S then it is also processed by the C pre-processor (which is often useful).
Depending on what you are actually doing, writing the code in C might generate good enough object code (and is easier).
OTOH I wouldn't even try to use an IDE's build scheme for anuthing complex.
Write your own makefile and linker script.
