Typically, the development tool itself (nmake, msdev, devenv, msbuild, etc.) will implement incremental building of individual projects (compiling only the source files that have changed since the last build). Since VB6 doesn't, VBP's Make VB6 step adds that capability for it:
http://www.visualbuild.com/Manual/makevb6.htm. If Gupta and/or CL don't provide this, you may want to wrap those with something like nmake and call that from VBP.