I would recommend have a pit dug to put the manure in (get someone with a backhoe to do this for you.) You can put lime, and then a then layer of dirt over a layer of manure, this will control both the smell and the flies.
In some areas (CA and AZ)you can get commercial dumpster service for manure removal, I think that's a excellent option if it's available in your area. You can go the less formal route and contract with a landscape contractor or anyone that has a front end loader and truck and get the manure hauled away monthly or semi-monthly.
Another option is to compost the manure - you can do this above ground, without the pit, with a tight wire enclosure. Lime helps with the smell, and the heat generated by the compost kills parasites. If you can manage to keep the compost covered, that helps generate sufficient heat for decomp and reduces the smell.
Also investigate feed through fly control, such as Raybon. It's relatively inexpensive, and greatly reduces flies. You'll have an easier time mucking, and the neighbors will thank you.