kuzman,
You can add any number of source folders you would like and just add them accordingly to your Java Build Path’s “Source” tab so Eclipse knows to treat the code like source… but they will all be compiled to the same output folder. If this isn’t a problem, then you are all set.
I’ve seen use things like “src” and then “src_gen” and “ejb_gen” and things of this nature to differentiate. If taht’s the case go ahead and create the folders, setup your XDoclet tasks to gen into appropriate dirs, and then go to your Project Properties > Java Build Path > Source panel, and add those dirs to the “Source folders on build path:” box.