Russ - Years ago when I did a partial draw down of my larger pond, I built a rock pile like you describe. Worked good until ice from several winters knocked a lot of the uppermost rocks off the pile. I takes real large rocks to withstand ice movement.
I suggest you not put any brush or items in the bottom of your pond. If you ever want to seine the pond this "trash" will be a source for lots of aggrevation. Seining would be easiest and most efficient if you partially removed at least 50% of teh water first and consolidate the fish into a smaller area. The "cover" should be confined in the upper layer of water.
During winter you will find that almost all the larger fish will be concentrated 85% to 95% of the time in the deepest, central, 50 diameter basin irrregardless of the presence or absence of cover.
PS: I you need advice on separating male and female bgill email me for help.
