I'm not sure what you mean but it's very easy to send different keystrokes to different windows with HotkeyNet. In fact, when I wrote the program, this is how I assumed it would be used. I was surprised when it turned out that most people use it a key broadcaster.

Here's an example. The following hotkey sends X to one window and Y to the second window when you press F1. There are three keys involved, and they are all different.

Code:
<Hotkey F1>
<SendWin aoc1>
<Key X>
<SendWin aoc2>
<Key Y>