Writing Progressive Metal

Writing Progressive Metal is one of the most difficult genres to write in rhythmically simply because of the fact that there isn't really any solid structure to lean on. The point of the genre is to expand your song from being a simple structured poem into free verse. Harmonically, it is a very vast genre as bands such as Tool and Dream Theatre both share this title. The main thing to keep in mind is to not limit yourself and restrict yourself to staying within the same time signature. What I have found in my writing is that if a melody or idea comes to my head, chances are pretty high that if I try using it in the song I end up loving the entire thing;
NEVER DOUBT YOUR MUSE.

I play guitar, so as far as writing drums the only advice I can really give is to do your best to make the 'feel' match what the rest of the instruments are doing. Check out bands such as Periphery and Tool for inspiration when trying to write drum parts in this style, definitely can't hurt.

When I write progressive metal guitar parts, again, I don't stress about what time signature I'm in. Go with the flow of your creativity. A good starting point would be figuring out harmonically rich chords. What I mean by that is find chords that compliment themselves, almost as if there is a melody hiding within the chord itself. It sounds strange, but you'll understand what I mean later on. Experiment with different chord shapes, and a good staring point would be 9th chords as well as Minor 7th chords. I highly recommend any drop tuning because I have found these chords will more naturally and organically reveal themselves to you after playing around in this kind of tuning for a while. Here is an example:

Experiment with arpeggiating the chord and sliding between them once you find a few you like. Also it's important that I mention that this is very much in the style that I write in, these chords are a bit more "bitter sweet" sounding than heavy evil sounding chords. For those, try Diminished and Augmented chords and arpeggios such as these:

Also experiment with exotic scales. I love Harmonic minor, Phrygian Dominant, and the Hungarian Minor scales and these are a great way to spice up your riffage.

Hope this helps! (tabbed all sheet music in Guitar Pro 6)