I want to duplicate a selection area in Krita and move it to anywhere I wish. The problem is, I can't do this simple manipulation because it creates an additional layer each time copied and pasted, which is not something I expect for ultra simple drawings such as black-and-white stickman sprite sheet. I have already used clone brush but it is not practical.
This cannot be done, and quite frankly there is no need for such a feature (pasting on new layer is already a special feature). While you're at it please ignore these "use photoshop" scrubs who think everyone can throw mountains of cash at software they don't even know how to use (or much less even need when there are free alternatives like Krita and GIMP...)
What you can do instead is use the "Merge with layer below" option.
Paste an item onto a new layer (ctrl+v) work it as you will, and then merge it down to the layer below (ctrl+e) problem solved. You can also simply forget the layers are even there (they don't make a difference after you save the file into a format that doesn't support layers like PNG or JPG)
You can't paste into existing layer in Krita. Sparr's workaround doesn't work in animation.
But there is one other workaround. The idea is to keep that layer visible only for a set of desired frames. After adding the pasted content, copy it into the desired frame using the "Copy frame" context menu option. Then go to the first frame of the animation and remove that pasted layer from the first frame using "remove frame" context menu option. That way, the pasted content will only appear when you want it to. Then once you are done with the pasted content, you can go to the frame where it needs to disappear and choose the "new frame" context menu option.
It isn't very intuitive, and once you remove all existing frames of a layer, the layer will lose its contents.