I'm not sure that I understand what you are trying to accomplish, but... From your description it sounds like you are confusing saving with duplicating. If you have some content in a keyframe, and then you hit F6, you will get a new key frame that will carry the content from the previous key frame. In other words, adding a key frame to a layer that contains something will cause that new key frame to contain the same content. The content of the selected key frame will be duplicated into the new key frame. Likewise, if there is nothing in the current key frame, adding a new key frame to the same layer will give you a new, empty, keyframe.
If you have multiple layers and are adding a new key frame to just one layer, that layer will now be longer than the other layers and the content of this active layer may now be out of synch with the content in the other layers.
Good luck with your project.