Hi,
mojoPortal is designed to be an application framework so my recommendation is to rework your application to be a plugin for mojoPortal and let mojoportal provide role based security and skinning as it was designed for.
I did not design mojoPortal to be a plugin for other applications, I designed it to be a framework for plugging in other applications/features, maybe its possible to do it the other way around but its not my goal and not my concern how to do it.
Best,
Joe