A few options:
1) Specify the path relative to the .bld file location, i.e.:
%PROJDIR%\Source
2) Add a project macro set to the desired value (on the Macros tab). This could be combined with #1 (i.e., create a project macro called SRC_DIR with a value of %PROJDIR%\Source, and then reference %SRC_DIR% everywhere it's needed).
3) Pass in the macro value on the command-line:
http://www.visualbuild.com/Manual?command_linegui.htm