One thing that’s very common among Unix libraries is that they are organized such that:
./ Makefile and configure scripts.
./src General sources
./include Header files that expose the public interface and are to be installed
./lib Library build directory
./bin Tools build directory
./tools Tools sources
./test Test suites that should be run during a `make test`
It somewhat reflects the traditional Unix filesystem under /usr where:
/usr/src Sometimes contains sources for installed programs
/usr/include Default include directory
/usr/lib Standard library install path
/usr/share/projectname Contains files specific to the project.
Of course, these may end up in /usr/local (which is the default install prefix for GNU autoconf), and they may not adhere to this structure at all.
There’s no hard-and-fast rule. I personally don’t organize things this way. (I avoid using a ./src/ directory at all except for the largest projects, for example. I also don’t use autotools, preferring instead CMake.)
My suggestion to you is that you should choose a directory layout that makes sense for you (and your team). Do whatever is most sensible for your chosen development environment, build tools, and source control.