Your task with an existing catalog will not be easy. You will only make it more difficult if you try this outside of LR. I do not know of Peter Krough's recommendations for file and folder structure, but that is not important. You can create any folder structure you like inside the folder panel of LR. From there is is possible to drag existing images from their present location to the new desired folder. If the Peter Krogh proscribed file and folder structure is not duplicated in the import options of LR, you will be wasting your time with a constant reorganization of files and folders after every import. LR is it's own DAM system and as such it may not be organizationally compatible with the Peter Krogh DAM system. That does not mean there is anything wrong with either. In the long run, you will be happier working in LR with a DAM system that is compatible with the LR workflow. I am sure there are many other principles from Peter Krogh's book that can be applied inside of the LR environment.
To summarize what LR does with the image files, it maintains a database of information about each file. One of the pieces of information is a pointer to the physical location of those images. If you move a file outside of LR, then the pointer gets broken and LR gets confused. This is why it is better to do all file operations inside of LR so LR can keep its reference pointers intact.
BTW, Welcome to the forum. You will find lots of help about this and other topics here.