Correct. ATC commands are bound to the top 1-0 keys. Numpad keys control the plane.
Personally, I find it handy to have a button on your yoke / controller to toggle the ATC window. You can just open it quickly when you need it and close it again without having to mess with the keyboard.
Like I said, 95% of the time, your reply to ATC will be #1. Of that remaining 5%, 75% of that will be 2, 3, or 4. I have all of those commands bound on my yoke as well. I can quickly pop open my ATC window, choose and send my reply, then close the ATC window without ever taking my hands off my yoke. Only when I need to issue more complicated commands (navigating ground at a large international airport, doing VFR approach callouts, searching for an alternate airport, etc) do I have to use keys 5-0.