In java project build path settings, you can point to external folders to build from.
"Link additional source: use this if you have a folder in the file system that should be used as additional source folde"
So you could have your C++ project pointing to the main folder, then create a java project in a different dir and then use the above mechanism to compile all the java source. Not a great solution, since you have two projects and two different working dirs.
What I can tell you for sure, is that you can only have one project per location on the file system, since eclipse creates a whole bunch of metadata dirs etc..
My only other thought is if you could create a project that builds Java and C++. Eclipse has the concept of builders and natures. Somehow you need a project with Java and C++ natures/builders...
I did a quick google and it looks like this post covers both of these options: http://lorinc.blogspot.com/2006/10/how-to-mix-java-and-c-code-in-singe.html