Consider the following ideas before you perform build management for UNIX and Windows together.
A Rational Synergy session on UNIX probably cannot see your work areas on the PC, and a session on the PC cannot see your work areas on UNIX.
Most sites probably have existing parallel makefiles for building on UNIX and the PC. If so, you can continue using your makefiles on both platforms. If not, perform the following operations.
When you update the parallel versions of the project, each brings in the appropriate makefile for its platform.
When you automate your update and build process, automate the Windows and UNIX jobs separately with shell scripts or batch files. You can also use a cross-platform scripting solution, such as Perl.