tim5901,
I am not sure what do you mean by configuration. Are you referring to using the same preferences in all your workspaces? In that case, yes, you can export/import preferences by doing this –
1. Open MyEclipse IDE
2. From menu options click on File > Import > General > Preferences and import the preferences you have already saved.
If you are not referring to preferences, could you elaborate what is the configuration you are referring to? Could you attach a screenshot to help me get a visual?