The most common directory structure has all Bitovi libraries at the root along with folder(s) for the app:
/root
/appname
/can
/canui
/documentjs
/jquery
/funcunit
/steal
stealconfig.js
js.bat
js
Sometimes this structure changes depending on the environment which is very easy to do now that Steal (via stealconfig) can map paths and modules the same way RequireJS can.