Despite the title summarizing the issue, let me express same thing with different words. I am new to krita(I am actually quite new to digital graphics design. Nevertheless, I have basic knowledge related to both 2D and 3D, given my little old experience regarding game making). I just wanted to dublicate a selection area and move it to anywhere I wish. The problem is, I can't do this simple manipulation as in my old MS paint days because it creates an additional layer each time copied and pasted, which is not something I expect for ultra simple drawings such as black-white stickman sprite sheet. I have already used clone brush but it is not practical. Thanks in advance!
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)
If you do not like this, bring it up for discussion in kritas development forums as a feature request.
This is a terrible workaround, but I have found that when I want to perform this operation I will paste into a new layer, then select the pasted area, then select the original layer, then delete the pasted area, then merge the new layer down to fill the hole.
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.