Eclipse is a really great editor, which I prefer to use, but the GUI design tools for Eclipse are lacking. On the other hand, NetBeans works really well for GUI design.
Echoing @Tom I'd use an external build tool (Maven 2 would be my pick). I've done this on projects before and as long as you don't walk all over Eclipse's .Xxxx files and folders you'll be fine. Then you get the full power of Netbeans (which integrates with Maven 2 really nicely) or Eclipse and also have the added value of an external build which can also be run by your CI tool. Everybody wins!
Define your project dependencies with Maven, and use it to generate project configuration files for both Netbeans and Eclipse.
Try to keep separate classes directories for Eclipse and Netbeans, since Eclipse doesn't like it when external tools touch its classes.