At one point in my game, I wish to pop up a help menu. QDK remembers how the how the window was last sized. Sometimes my window appears minimized and the player cannot see the message. Can I specify a window size like I do a .jpg and can I specify that it be maximized?

I don't think so.

I don't really understand what you mean, as from my memory you can't minimize the help window. Could just be my dodgy memory though.

You could always have the help stuff inside a text file, and just launch this file when they type help!
Or display help to the main window.