System Exec is like starting a program from the DOS prompt. For example, from DOS you can open a specific VI by typing LabVIEW.exe filename where filename is the VI you want to open. Different program may or may not open files this way. If the program does, it may or may not accept other command line parameters. You cannot, for example, open Excel from a command line, modify some cell, run a macro, and then save the new file. Control over most programs, to this level of detail, must be done with some other mechanism. For many programs, this mechanism is ActiveX. For others (mainly older apps) it might be DDE. LabVIEW provides the system exec, ActiveX, and DDE. You have to know about the application and what it supports. The worst is a windows program with no built in support and you have take control of the mouse, simulate clicks, etc. There is no universal method because it is up to the developer of the application to decide what kind interface to provide. If there is some specific executable that you need to run, what is it? If it's some popular commericial application, you may find someone here that has experience with it. Otherwise, your best bet is the documentation provided with the app.
