Go into "File/Project/Save As..." and you can save the project file (.dcp) for your builds. That file contains all compiler settings, including project macros. You should be able to store that in the same directory as your source code, and even eliminate the need for absolute pathnames (but you might need to edit the .dcp file manually for that). You'll also want to have your custom LIB.DIR file there to point to the directory with your libraries.
You should also be able to use that .dcp file for command-line compiler builds with "dccl_cmp.exe".
And consider upgrading to the latest release available on digi.com -- Dynamic C 10.72B. And if you're comfortable with Git for version control, you can access development builds on GitHub: https://github.com/digidotcom/DCRabbit_10