BB - you need to set up your new folders in LR, (right click on the Mac when you are hovering over the folders in the Library module) - the same goes for any other new folders or sub folders that you need - do this in LR - if you want to move files from another folder to a new folder - do that in LR - physically drag them into the new folder from the old
ricks - once you work on a file, (image), in LR - LR attached another "file" to it that records all the work that you have done on that file - the original image is left as it was imported, (non destructive editing - a major feature of LR)
If you move files around in your operating system, (i.e. not in LR) - these files get separated from the original image and LR does not know where you have moved the original file, (image), to - because you performed the action outside LR.
you can back track and try to get everything back in place - but it is sometimes easier to start again depending on the number of images involved
this involves deleting the (non existing image that appears to appear in LR - usually with a ? in the top corner), from LR, (BUT NOT FROM YOUR HARD DISK) and then reimporting all the (LR) missing images back into LR - (plus you will have to do all the adjustments that you did before in LR, if you want the same finished images) - you can try it with one image and see how it goes BUT it is easy to start accumulating lots of "funny" folders with no images in them if you are not careful - particularly if you have created the same named folders in LR and ALSO using the finder in the OS - it can get frustrating .......... and you can end up with duplicated images in you do not follow the BASIS..BASIC LR rule as explained above
as Paul indicated synch does work, (but can take time), - after which you then need to check your folder and sub folder structure