Progressive Rock is an awesome genre, nice to know that there are composers who aren't afraid to write for it!
My advice, especially for a genre & composition this complex, find the "hook" you want and let that carry you through. For example, if you feel like the harmony is the "core" of the piece, then find ways to spotlight that as you write the other stuff. Or if you want the drum riff to be something that carries the listener, work that into and around some of the other things. There are endless possibilities, and that's the cool thing about this genre and how it works. Think like this, "In 50 years, when I'm famous for this song, what do I want people to start humming this song and everybody immediately knows what they're humming?"
So to answer your question straight out, it's hard to tell whether a piece is "going somewhere" until you let it take you all the way to the intended destination. Sometimes it turns out to be nowhere, other times it's where you expected, and other times it's not even remotely where you'd thought but it's cool anyway. I guess I'd say go for it - pick your focus and have fun, and let the music "guide you".
I feel like a jedi from Star Wars... "Use the force... Let the force be your guide..........."
Gustav Johnson