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Just plain simple, follow the tutorial on this website to integrate openCV in your project, which also works for later versions:

http://www.anlak.com/using-opencv-2-3-1-with-visual-studio-2010-tutorial/

To then destinguish between both libraries, make use of the library namespace, meaning you should use the following code structure

yourLibrary::fuction1()
cv::function1()

Which could be the same function, but implemented in other libraries.