However, you might find it useful to get AutoIt for its AutoIt Window Info Tool, which can be used to get information about the windows that you are trying to automate.

I use http://www.catch22.net/software/winspy-17 to find the info I need (normally the Window Class, and the Window's title).
(Or you might already have the Spy++ utility that ships with Microsoft Visual Studio.)

Then you call Win32::GuiTest's FindWindowLike() to get a handle to the window. Then you can manipulate the window.