Here are two ways of doing it.
1. A VI's front panel will be displayed at the screen position at which it was last saved. If you have two different VI's which you always want to display at specific locations, just move the panels where you want them and resave the VI's. The VI's will now always open at their new locations, either in the Labview environment or after you recreate an exe using the application builder. But if you distribute your application to a machine with a different screen resolution, they may not display where you expect: e.g., going to a lower resolution, some of the front panels may be off the screen.
2. If you want to move them programatically, look at using Get Panel Size.vi and Resize Panel.vi in C:\Program Files\National Instruments
\LabVIEW 6.1\vi.lib\Utility\victl.llb. By keeping the difference the same between top and bottom and between right and left, you can use Resize Panel.vi to move the panel, not re-size it.