Greenfoot is java programming. I would think that as long as your project in Eclipse was a java programming issue, that it would not be a problem. Just make sure you supply enough information (project info, code, errors, etc) and explain your issue in a detailed manner to give yourself the best chance of being helped.

I've found in general that on StackOverflow it's fine to ask questions as long as you are very precise about what is going wrong and give a short but complete code sample showing what you've tried. I.e. if you try something and it doesn't do what you expect, it should be ok to ask about it on StackOverflow. If you just want general "tell me how to do xyz" then it's probably not the place. A big part of the process is learning the right way to ask your questions. (See here for some guidance). You are allowed to post any programming questions here, but I doubt you'll get better answers than you would if you posted apropriately on StackOverflow.