Here's a very good tip (I think):
Don't try to have too many themes going on in your song. You may end up just putting random riffs in that, while good on their own, don't relate or add much to the song itself. You can use a lot of dynamics and variations on a theme to write a song.
This tip basically wrote my last song:
http://www.acidplanet.com/artist.asp?PID=930310&t=2407
Go there to hear it for a good example of what I'm talking about (I barely realized I did this until one reviewer pointed it out).
It's a 12:32 song that has one solid theme that dominates while there are 1 or 2 others that are there to spice it up. It's based on a minor I VII IV(maj) progression, but I expand making an almost 12 chord progression with it. Off of that progression there are many parts that I made that go over it: a tremolo picked melody with a harmony, an acoustic picked melody, a synth melody, a picked electric guitar melody, as well as a vocal melody with a harmony.
Summoning is band that is very good using a strong main theme with many variations. They write some amazing music. Check out their latest "Oath Bound." They influenced this song greatly.
EDIT: Hah, sorry that doesn't answer your rhythm question.