The autotools chain is quite a patchwork system -- there isn't enough structure in the toolchain for an IDE to "import" the project consitantly and correctly. However, some IDE's (e.g., eclipse and netbeans) can import them, provided the build script follow certain popular conventions.
If you want to work with code in the most robust manner (cross platform, cross IDE etc) I would find a set of tools that are designed to be portable.
So, what I am driving at is that you need a robust build system. A robust build system would compile the same code base on any OS/IDE. In order to achieve this you need to be able to specify your build needs at yet a higher level of abstraction. Tools exist to do this, and in the C/C++ world CMAKE is the popular choice. Once you have written a CMAKE description of your project you can target any IDE.