appropriate substrate depth

[lmetcalf]

Hello all,
Im setting up a new FOWLR aquarium, 30gal. I've heard differing opinions regarding how deep my substrate should be.
The issue is regarding anaerobic bacteria and their usefulness. In my understanding (please correct me if i've got this wrong) they have the ability to utilize ammonia (I think, or some other bad chemical) and create inert nitrogen gas, and exist in deep substrate where oxygen is scarce. Unfortunetly they can produce trace ammounts of toxic stuff too. I read somewhere that they might not actually be able to metabolize ammonia in an aquarium because of the high concentration of oxygen.

This is a lot of information! So i don't know what to do. Im not using an undergravel filter. (just powerfilter and protein skimmer)
Should i have a 1/2 inch of substrate or 3 inches? or something inbetween??

Thank you for any and all input!!!!!