why does boolean difference make a copy

I have been suffering for the last 5 hours.
How come when I use boolean difference to subtract an object from another object,
I end up with 3 objects… the original two objects and the new composite of the two objects. I get the part about moving the cutout object to another layer or hiding it…
…but now I am still stuck with two separate objects… the original object i wanted a shape subtracted from, and the weird shaped composite of the two together. It looks like a randomly broken piece of the original object.

I thought I could get away with somehow merging the original object together with the new weird shaped object by moving them around or deleting vertices but it looks messed up no matter what a seam is always showing… and I have too many vertices to deal with to have to manually merge them one by one.
Please help.
does this make sense maybe i will post pics later if it doesn’t.