You can't control ZBrush from the command line beyond launching it with a file. You can write an executable (or for that matter, a DLL) that launches ZBrush with a zscript but I don't know if you could launch more than one zscript this way. The Windows code would be something like:
static const char *zbrushFolder = "C:\\Program Files (x86)\\Pixologic\\ZBrush 4R3";
static const char *zbrushExe = "zbrush.exe";
static const char *scriptPath = "C:\\Users\\Mark\\Desktop\\TestZScript.zsc";//if just a file name then ZBrush will look in the default location 'ZScripts'
WinMain(HINSTANCE hInstance, HINSTANCE hPrevInstance, LPSTR lpCmdLine, int nCmdShow)
ShellExecute(NULL, "open", zbrushExe, scriptPath, zbrushFolder, SW_SHOWNORMAL);