Howdy, Duane.
Maybe a dumb question - do you have fish in the pond? If so, running aeration 24/7 when starting up in an older pond with a large muck (old organic deposits) can be a bad thing. If your pond had no O2 in the deep water next to the muck, those organics were decaying anaerobically (slowly wrt the rate that is achieved through aerobic decay with aeration) and possibliy building up gases like H2S that are deadly to fish. That's why the advice usually given for starting aeration on an older pond is to start slowly, like 15 minutes a day a first and gradually work up the length of time, to release those gases in small quantities.
Here is just one post of one of our aeration pros (Ted Lea) advising that:
Aeration Startup Here is a post you may find interesting that talks about how muck is reduced through aeration:
Clean Bottom. And here is the aeration post that I personally have found the most useful overall:
(Seasonal Aeration Starting & Stopping). I'm not sure what depth would be optimum, but one piece of advice I can give on placing your aerator output (diffuser/airstone) at: you want to avoid having it directly contact the bottom muck. To avoid stirring up the muck off the bottom and creating a cloudy water problem, airstones are often placed inside weighted 5 gallon buckets (mine is) and diffusers can be strapped to a broader-based object (we have seen pictures of garbage can lids and car/truck wheels used); in either case the object is to place the air bubble source near the bottom (at whatever depth) without actually touching the bottom mud/muck.
P.S. What kind of aeration system are you running? That would help the pros (not me) tailor advice for you.