I did that a while back:
http://mcuoneclipse.com/2012/02/13/make-my-make-with-eclipse-and-mcu10/
It works the same way (with make files) for S12/HC12, as the build tools (compiler, linker) are command line tools. Actually the command line commands are pretty much the same as for S08, so can be used the same way.
I hope this gives an idea?
If there is enough interest (and I find time), I could set up someting for S12 similar to what is describe in this series (but using S12 instead of ARM):
DIY Free Toolchain for Kinetis: Part 1 – GNU ARM Build Tools | MCU on Eclipse
Of course the compiler would not be free ;-)