Hi,
You can do it with code in your app like this:
edContent.WebEditor.ScriptBaseUrl = WebUtils.GetSiteRoot() + "/ClientScript";
although the above example is just setting it to the same value as default.
I've really only completed phase 1 of my plans for the editor. When I get to phase 2 I want to implement a consistent way to upload/browse/link to files across editors as well as make the format/template toolbars use the same sets of format/templates. At that time I will also look into making t easier to use outside of mojoPortal. Maybe I will make it check a web.config setting for script location.
Hope it helps,
Joe