If you're on a Linux system, learn how to use Makefiles for building since they're generally useful for lots of things. Cmake is becoming more common and does some good things, but I find it very hard to use/debug (and you might find yourself debugging the Makefiles it generates anyway). It helps if you already know how to compile/link C programs...

How to incorporate external libraries depends on if they're header-only, shared libraries, or static libraries (do people still use static libraries?). pkg-config is your friend!