At this point, you might be thinking to yourself something along the lines of "Hmmm...I bought this product, which is supposed to publish everything, to publish my fabulous and unique _____ server. Now you're saying I am the one who's supposed to pick and choose?!?!" Well, in short, yes. The long answer, though, is that UAG is certainly not "supposed" to publish "everything". It's extremely versatile and flexible, but each application and service has its own characteristics, and some can be difficult, or even impossible to publish.
Some applications will require careful analysis and planning and, occasionally, some trial and error.