When using Eclipse CDT without this plugin, you have to choose between a "managed make" and a "standard make" project type. The first one causes severe restrictions on the build system of your project and will usually not be sufficient for larger projects as you cannot provide your own Makefile. The second one does not have this restriction but has a less sophisticated integration with the Eclipse build system.
The autotools plugin combines the advantages of both modes in one new mode: You can use your own Makefiles created by GNU autoconf and automake but Eclipse will still take care of automatically building the project.
This mode works just fine for existing projects: I checked out the source code of suPHP from the repository and converted the project to an autotools C project (this can be done using the File -> New -> Other... menu). Without much need for configuration Eclipse ran the configure script and built the project. After the automatic build process completed the autocompletion feature worked like a charm: It provides autocompletion for methods and attributes of an object making C++ development nearly as much fun as Java development.
By the way, have a look at the ChangeLog plugin also provided by Fedora Eclipse. It is only a small plugin but can be very handy when documenting changes.