Ok, that info about analogWrite() and digitalWrite(). I had figured that was the case, but, like I said, I'm very new to all this. 
Polling sensors and responding on a certain interval raises another question. I see that there are chips people have added to arduinos such that they "know the real time" in a sense. What is the timekeeping ability without this additional chip? Assuming I am running lights off time of day (i.e. "turn on at 8 PM") instead of some preset interval (i.e. "turn on 12 hours after you last turned off") then I'm guessing I want one of the external time chips. Is that an accurate statement?
Also, regarding a wavemaker. There are lots of commercial units out there that feed PWM to a DC motor to ramp it up and down in speed every few seconds, so I was assuming I would duplicate that approach. But, the thought someone mentioned above (use a servo to move a paddle) is interesting. The first tank I'll be trying this on will be small (15 gallons) but eventually I want to use this controller on a large tank (300 - 400 gallons) so at that point, I would need a pretty big paddle and a really beefy servo. The only sources I know of for servos are for little hobby servos from R/C stuff, does anyone have a source for more robust servos? Or even some sort of linear actuator?