I have batch file that sets up the desktop environment for me when I am writing code. The file is named: SetEnv.cmd and it opens 3 other windows:
Check out StartX. I haven't used it, but it looks like you can use it to launch an application with a specific position and size.
StartX, a very simple utility to allow you to call the CreateProcess API from the command line.
Some of its commandline parameters:
StartX ["title"] [/Dpath] [/MIN] [/MAX] [/Px,y] [/Scx1,cy1]
x,y: Specifies the x and y offset, in pixels, of the upper left corner of a window if a new window is created. The offset is from the upper left corner of the screen.
cx1, cy2: Specifies the width and height, in pixels, of the window if a new window is created.