In my opinion, organizing by folders is a very sub-optimal way of doing things ... in other words, takes a lot of effort and doesn't provide the benefits of using Lightroom tools for organization. (In addition, sometimes Lightroom beginners seem to make serious mistakes when moving folders from here to there and we don't want that).
So, I would advise you to leave the photos in whatever folders they are in now; and then use Lightroom tools — specifically keywords and other metadata (captions, titles, GPS locations) — to achieve organization and for searching.
Note, I do not recommend collections as the method of organizing. While much of the things you can do with collections overlaps heavily the things you can do with keywords, in my opinion collections (note: I am referring to regular collections and collection sets, and not the smart collections) have a major drawback, and that is that the collection(s) that you put a photo into exists ONLY in Lightroom and can never be exported; whereas if you use keywords this information can be exported for others to see if you so desire. Further, there are more search tools in Lightroom that work with keywords than there are search tools that work with collections. So, my opinion is that keywords are preferable to collections, and the only thing I use regular collections and collection sets for is to make a "creation" in Lightroom ... a book. slideshow or web page (again Smart Collections have a different purpose and are useful as searching tools).
Thank you! I have just started using Lightroom this week. I hadn't thought of using keywords instead of collections. And by virtue of its name, I now understand that a collection should be used as you have described. Interestingly, I have found, after reading your response, that my photos did import from my other program with the keywords that I had added previously. So, perhaps a lot of my work is done. Once I keyword all of the photos, will I be able to just delete the collection sets and collections without causing any problems?
Sure if the collections and collections sets have no further value, you can delete them without problems.