Dusty cover: As you take the cover off, give it a good shake to get the dust off. The easiest way to wash the cover is to leave it on the boat, wash the cover, let it dry, then wash the boat.
Threaded hole: is the hole dead center? It sounds like the second, inside drain plug. It is common for there to be one drain plug in the transom, installed from the outside and then to have a second drain plug, just forward of the engine (on a V-drive) that installs from the inside. The inside drain plug usually has a "T" handle on it so you can install/remove by hand.