The main Problem is that Apple Script Editor doesn't know any of the Names "App" nor "App 2" so if you run the script it asks you to select where App is stored and then replaces "App" with the Actual Name of the Application. This also happens for "App 2".
So if you two times select the same Application (which is what you're trying to do, according to your mentions) it will both times remove the Names "App" and "App 2" with the same Name of the Actual Application.
Or if you use App as an Abbrevation for the Actual Name of the Application it knows the Application in First Statement but not in the Second so it will Ask just one time and just replace the "App 2".
To do what you want i recommend you to change your Script to something like this and try it that way (not tested):
tell application "<Name of Application>" to activate --open first Window
tell application "<Name of Application>" to activate --open second Window
tell application "System Events" to tell application process "<Name of Application>"
set position of window 1 to {8, 22}
set position of window 2 to {914, 22}
end tell
if this doesn't work maybe you can adopt this Script which moves two open Finder Windows Side by Side.
property monitor_width : 980
property monitor_height : 768
set the startup_disk to (path to startup disk)
tell application "Finder" activate
set visible of (every process whose visible is true and frontmost is false) to false
-- BOTTOM WINDOW
set this_window to make new Finder window
set the target of this_window to the startup_disk
set the bounds of this_window to {0, (monitor_height * 0.55) div 1, monitor_width, monitor_height}
set the current view of this_window to column view
-- TOP WINDOW
set this_window to make new Finder window
set the target of this_window to the startup_disk
set the bounds of this_window to {0, (monitor_height * 0.06) div 1, monitor_width, (monitor_height * 0.53) div 1}
set the current view of this_window to column view
end tell
Source: http://hints.macworld.com/article.php?story=20011127022706921