Non-standard path to Quartus/SOPC files

I have a working FPGA project in Quartus II (10 SP1): simulated, synthesis/place/route, running in the lab. In fact, it is purely an SOPC project - built and configured in SOPC builder. Quartus II is only used for synthesis/place/route, etc.

The problem is: I am required to have a very specific directory (linux) structure, similar to the following:

Project root: /data/Projects/MyProject

Non-VHDL Quartus/SOPC files: /data/Projects/MyProject/FPGA/Altera/

VHDL source files: /data/Projects/MyProject/Source

Does anyone know how to make SOPC builder generate/update the files in the VHDL source directory defined above, yet have the project files (QPF, SOPC, and supporting files QSF, TCL, etc) stored in the Non-VHDL directory?

Thanks!