First, you need to make sure the MPI executable is properly configured. In the Compiler and Support Options window, make sure that the MPI Executable and number of images are properly set to your liking. The defaults should be sufficient.
Second, you'll need to enable launching using MPI for your particular project. In the Project Options window, go to the "Launch" category. You'll need to click the options "Launch Using Message Passing Interface."
Finally, you need to link the MPICH library to your executable. The MPICH library, on Debian/Ubuntu, can be linked by adding the following flag to the Linker box under Compiler Flags in Project Options:
It sounds like you should have most everything working already on Linux, though, if it all works through the command line. I should note that Simply Fortran's debugger will not work properly with MPICH controlling your executable. It would be best to debug the program as a single-thread/single-image implementation prior to moving to MPI.