You could use mouse and keyboard messages to control the program. This is pretty hackish, but it does work. For example, the mouse cursor can be control with Cursor.Position.
This might be easier in C++, though. Basically you grab the handle of the window and use SendMessage() to let it know what you want. WM_LBUTTONDOWN for example.
[DllImport("user32.dll")]
public static extern void SendMessage(IntPtr hWnd, int Msg, int wParam, int lParam);
The lParam parameter contains the x/y cursor position. I've seen a minesweeper bot that uses this approach combined with some image processing logic, but if you want a simple hack, you can just hardcode the positions of the buttons.