The best way to integrate it is not to actually integrate Mephisto and
your app at a code level, but run them as two separate apps and just
make them act like they're part of one site. The user can't tell the
difference unless they look very closely.
For example, take a look at www.BuildingWebApps.com. Click on the Blog
tab, and you'll see the blog, and the URL will be
blog.BuildingWebApps.com. The blog is running Mephisto as an entirely
separate application; it has just been styled to look like the main
app. The DNS directs blog.BuildingWebApps.com to the server running
Mephisto, while www.BuildingWebApps.com goes to the main app server.
P.S. There is a separate group for Mephisto that you may find to be a
better place for this discussion.