Something seems to be destroying the formatting of your posted scripts, so I'm guessing here, and is appears Khat came to the same conclusion on where you are trying to go.

It looks like you want the small window to be 33% of the large window at 360 pixels high. To maintain resolution it needs to be 640 pixels (1920*0.3333...) wide.

The following has the resolution set that way.

Code:
//----------------------------------------------------------------  
// SET PIP CONFIGURATION   
// Usage: <SetPip BigWindowName LittleWindowName>   
// This command is called by <Hotkey F1> which is defined below.    
//----------------------------------------------------------------   
<Command SetPip>
      <TargetWin %2%>
         <SetWinSize 640 360>
         <SetWinPos 1280 720>
      <TargetWin %1%>
         <SetWinPos 0 0>
         <SetWinSize 1920 1080>
      <TargetWin %2%>
         <SetForegroundWin>
         <UpdateWin>
      <TargetWin %1%>
         <SetWinRegion 1280 720 640 360>
         <SetForegroundWin>