Well the popping noise could be happening when the auto function initiates. I had a sub that would do the same thing. If the sub doesn't recieve a signal for a few momments like in a very quiet part of a movie it would shut down and pop when it did. You can leave it on and it shouldn't be a problem except for the obvious extra use of power and in the life of the amp but you can do it. If it still pops then you have another issue.
I had an 8" sub that, whe left in on, would draw about 10-12 watts, which where I live is about $15-20 dollars a year. If you want to save that money on electricity, leave it in "on", but put it on a switched outlet or power strip. Only turn it on when you're using it.
Thanks for all of the information. I'm starting to think that the pop is the sub actually turning off. It's a different sound than when it turns on but it would make sense that it would be. When it turns on you hear the relay click followed by a surge of bass. I'm going to monitor the on/off switching when in auto mode everytime I hear the "pop".
Mine always shut itself off during periods of no bass. I leave it on all the time now. I have a seven year warranty on the amp though. I don't think it wears on the components to leave it on all the time.
I dont trust mine to not burn down the house so I unplug after use, its a 6 month-old dayton plate amp and it is still warm on auto on and the sub or amp, not sure which is the culprit, emits a barely audible drone.