I can confirm that yes is will work well alongside the ATOM SDK. OpenCV is an excellent library, should you have any questions on implementation please let me know.
As far as the ATOM SDK is concerned, think of it as your authentication engine. You can create any C++ application you wish, using any library which you have license to and it will work wit the SDK. If you run into any linker issues please feel free to post the details here. Best of luck.