Controlling an unknown program

I am currently working on a college project which needs me to control an external program that I have downloaded, with a GUI program that I have written. I am not sure exactly how to approach this since my efforts to get this working seem to have been in vain.

All I need to do is send simple messages like button clicks to the external program's controls. This on it's own is not difficult, I was able to send messages between two test programs that I have written where I know all the control ID's. Where I get stuck is finding these ID's on the external program. I've tried spy++ programs but all they give is the thread and that changes every time the program is opened.

Is there a better way to accomplish this task or am I going in the right direction and just need a few pointers on how to get this job done?

Please, I want as many opionions as possible, this is costing me valuable project time being stuck at such a trivial problem.

Spy++ can give you the IDs, class names and titles of windows...

The control ID's are always the same as the thread ID's when I check them with spy++, therefore, since the threads are always changing so are the ID's... I was wondering if there was a better way to do this...

Strange. Very strange. What program is that you're trying to control?