Not sure about the 'multiple files without it popping on and off' part, but you can use ExecFile to run an exe with commandline keys.
Example.
ExecFile Chr$ ( 34 ) + "C:\Program Files\Blitz3D\bin\blitzcc.exe" + Chr$ ( 34 ) + " -h"
Should run the Blitz 3D compiler and show the commandline help.
Example.
ExecFile Chr$ ( 34 ) + "C:\Program Files\Blitz3D\bin\blitzcc.exe" + Chr$ ( 34 ) + " -h"
Should run the Blitz 3D compiler and show the commandline help.