How can I know what changes are being made by an exe in Windows

This is a very broad question, and so I'm really just looking for what directions to look in.  Here's my problem:

I'm running Windows 7 64 bit.  I have a USB pen input device that is extremely useful, but the assocaited configuration software for the device has some unfortunate limitations.  I'm looking to take the long road in coming up with a potential fix/hack for one particular limitation as I feel it could be worth it in the end.

There is a stand-alone configuration utility for this device that allows the user to change some use settings for the device.  One particular setting must be changed fairly often to use the device most productively.  The problem is that it takes several clicks to get to that setting, so changing that setting is tedious.  

The configuration utility surely has only a limited number of ways it can be 'recording' the setting change (which is, by the way, persistant after reboot).  What I want to do is know what tools are available for me to somehow get continuous snapshots of the environment so that I can detect "what happens" when I change that setting.  With that information, I hope I can develop a separate tool that performs this action much more effeciently.

(I actually did use hWnd references and some C++ unmanaged code to automate the launching of the program and delivery of the user to the proper setting location in the UI, but this still is fairly clunky and somewhat slow... and I'm looking to build something much more elegant.)

Thanks,
-iluomo