For a Makefile project, the Project Properties look a bit different. To bring up the project properties dialog, rightMouse on the project in the Project Explorer view, and choose "Properties" at the bottom of the context menu.
Set up the includes to point to your MPI (or OpenMP, or UPC, or LAPI) include path.
You set up the PLDT preferences the same way as for regular C (Managed Build) projects.