Pedarrin2 is correct that for design purposes, a gravity pipe is not intended to run full. Now, that is not to say it won't if the facility experiences growth and the effluent pipe is not replaced.
Under this condition you will use another equation such as Hazen-Williams.
Mannings equation has already been provided, and the wetted perimeter formula is not a simple equation relating to the depth of flow. You can see that by the pipe geometry using the depth of flow you will have to calculate an angle between the water edges first in order to calculate the wetted perimeter and area. Here is a link to a manning's equation calculator to make things easier. You should understand the equation first; but, the calculator can make things easier.
Now then, under non full conditions, you will experience the peak flow through the pipe when the pipe is approximately 94% full.
The "n" value is also based upon the pipe roughness (ie friction loss). PVC and steel pipe have an N value of 0.009 to 0.011, Conc pipe = 0.011 to 0.013, etc. As the pipe ages and increases in roughness, the value will increase to the high end.
Getting past your first question and into some of the latter responses. You need to look more at the flow entering the treatment facility based upon population, industrial flows, inflow/infiltration, etc as stated above. You can perform some flow measuring for your existing facilities and base future expansion upon your results. If you size the facility for the volume the pipe is capable of you will probably drastically oversize your treatment facility and not get the treatment result you are looking for.
If the high flows are intermittent, you might consider some flow equalization storage or bypassing with primary treatment (if allowed in your state).