Delamite

So I have a program that if it's the selected window any keystrokes open a command line. The same goes for another program that I run side by side, but the issue is typing in both manually whereas I'd like to have autoit detect whether I'm using either window and subsequently when typing a command line (only alpha non-numeric), the script will detect, copy, and enter it into the non-active window; and vice versa. Is this possible? I have many other windows open including chat, email, etc that I don't want to confuse auto-it with typing in general.