Use AutoHotkey to run TT as mentioned above.
Once you've got it set up to run (and autoclick no on the save state box) then just RUN; c:\.........\AutoHotKey.exe to start it embedded.
However, be warned that TT will not run full screen embedded. And if you choose 800x600 for example, you will lose the bottom of the TT screen. I found 640x480 on an 800x600 screen is OK if you don't mind the blank spaces bottom and right.