It's not clear to me what you're trying to do...

Do you want to modify gcc so that it outputs different assembler code?

Or do you want to modify the assembler code created by gcc, then assemble it?

Either way, I don't really see why you would need to modify the gcc source code.

To modify assembler code created by gcc on the fly:

gcc -S hello.c -o - | sed 's/Hello, world/Goodbye, cruel world/' > hello.s

(That was hard, wasn't it?)

To modify and assemble asm code created by gcc:

gcc -S hello.c -o hello.s
vi hello.s              # edit hello.s
as hello.s -o hello.o   # assemble with the gnu assembler
gcc hello.o -o hello    # link
./hello