It's usually not a good idea to change locations of external libraries. Some libraries automatically put themselves in include paths of compilers but for those that don't, adding their paths to the compilers' include paths is always a better idea.
For example, in gcc, you can
gcc -I/your/header/directory to include your directory. Usually people put those info in the Makefile. This way, you can put external libraries' source code in your repository and just tell compiler to also look for the headers there. This way, when setting up a new working environment, all you have to do is pull from the repository.