Several options. but first you need to deal with ones you have already imported into LR and subsequently moved them in Finder. Once these are re-linked in LR, you can, from within the LR Folders Panel, put them into one or more folders on your NAS. The best way to do this depends on your situation. but first let's talk about the images already in LR
1) have you done much work in LR on these images (keywords, stat ratings, adding to collections, adjustments in the develop module, etc.?
2) Are the folders in LR folders panel that contain your images showing up with"?"'s About how many folders are we talking about?
3) For folders showing with "?", What exactly did you do with Finder after you had uploaded the images into LR? Renamed folders? Moved Folder? Moved images between folders? Something else?
Once those missing images and missing folders are resolved, we can deal with images not yet in LR and we have a couple of options.
Option 1 - organize them into the desired folders using Finder and then import them into LR. Use the 'ADD" option in the LR Import dialog. If you had organized them in Finder onto the NAS, you are done. However if you organized them into folders on some other drive, after import, use the Folders panel in LR to drag the the folders over to the NAS.,
Option 2 - Import all "New" (i.e. previously not imported) photos into LR using the "Add" option. Then do the reorganization using the folders Panel. In this process you can create new folders on the NAS and drag image into them using LR, you can rename folders and then drag them to the NAS, you move images from one folder to another, Etc. Just do this in LR and NOT finder. This may be a more convenient option as you can sort those images by capture time or deal with them in their current folder structure.