I think the first thing to point out, and you may already understand this, is that Photoshop by itself cannot edit raw image data. Photoshop cannot save raw images. So if you open an image in Photoshop from Lightroom and make additional changes in Photoshop, it is necessary to create the PSD or TIF file. Otherwise, you would lose all of the work that you do in Photoshop.
As far as JPEG images are concerned, I don't create them and I don't make them a part of my Lightroom catalog. I do create JPEG copies when I want to share an image or group of images with someone that includes all of the adjustments I have made in Lightroom. If that postprocessing included Photoshop, then the JPEG is created from the PSD or TIF file. Once I have shared that JPEG image with another individual, or posted it on the web, or sent it to a lab for processing it is discarded. I have no need for it. I can always generate another JPEG when it's needed. There just isn't any need to clutter up a catalog with a lot of JPEG copies.
If I send an image to Photoshop from Lightroom, when I am finished with the work in Photoshop I choose to save the Photoshop work as a TIF image. In my Lightroom options I have chosen to have it stacked with the original. I place the TIF image on the top of the stack, knowing that it's there if I need to go back to it. But I only have the one image that displays in Lightroom.
When transferring an image from Lightroom to Photoshop, Camera Raw is used by Photoshop to interpret the adjustments that have been made using Lightroom, and to create an image that is compatible with Photoshop. It is no longer raw image data. So if you are going to use Photoshop extensively in your photofinishing workflow you will have to accept the fact that there will be a second copy that will include the Lightroom adjustments plus all of the work done in Photoshop. But unless you have some compelling need to include an additional JPEG image in your catalog, I suggest that you not create JPEG's until they are needed. Use them for their intended purpose and then delete them from your system. They don't have to be part of the catalog at any time.
can I disable so that these duplicates do not appear in the original Main folder?
They may not be duplicates but rather just LR showing ALL images from all sub-folders.
To change this- In Lightroom Menu [ Library > Show Photos in Sub-Folders ] Remove the check mark by clicking on this menu item.
Some other suggestions-
Always open images into Photoshop by using "Edit-In" from Lightroom. (from raw, a pixel derivative image is created first)
Then do not use "Save As" in Photoshop- instead just use "Save" (& close) for the PSD/TIFF to appear in the LR library.
Use Lightroom "Export" to create JPG derivatives from the Psd/Tiff images. (why keep multiple jpgs when they can be exported by LR at any time?)
Easily use LR filters to search specifically for psd/tiff/jpg images in the one folder if needed. (and use Stacking to show/hide same image multiple file types )
Do not re-edit psd/tiff images in LR if you wish to preserve layers in a psd/tiff file. Do all LR development before edit-in PS.!
Here's the problem. Now in the Main category I not only have a .nef file but a .psd and .jpg thumbnail showing up in the Library view. This is just very confusing and cluttered. What option, if any, can I disable so that these duplicates do not appear in the original Main folder? I know I can not Stack them since they're in separate sub-folders.
The idea of putting these different files (nef and psd and jpg) into different folders is archaic ... in fact, the idea of using folders to separate these derivative versions of your original NEF, now that you have Lightroom, is completely unnecessary. If you are in Lightroom, you can create a filter (which can be reused over and over again) to show you only the RAW, or only the PSD. In addition, the idea that you need to save a JPG of one of these photos is unnecessary, as Jim Hess explained. The JPG derivatives of these photos are temporary, they should exist for as long as you need them, in a separate location, and then deleted (if you are sending JPGs to some other place, stock agency, e-mail, etc., you don't need to save these JPGs.)
So, in a way, I am recommending a mental paradigm shift, as well as using Lightroom more efficiently, as the solution. I am not recommending using different folders for JPG, PSD and NEF, nor is there a way to automatically have Lightroom put them into these folders.
Thanks for the suggestions. The tick mark for (Show Photos in sub-folders) was what I was looking for.
For my purpose I do have to create .jpgs and a .psd along with the original RAW file, and do delete the .jpg's after the agency has selected the ones it wishes to have in their library. I use an action on the .psd file while in PS to create these according to their specs and to apply sharpening if needed. Using the sub-folders for the .psd and the .jpg is just my (old way) of being able to keep things straight when dealing with so many images over prolonged periods of time.
I also made the mistake of unnecessarily Importing the .psd and .jpg files in those sub-folder, at least from a previous group of edited pics. Will work on improving my workflow!
I'm glad you got things sorted out. As I often do, I read through your initial post rather quickly and missed the fact that you needed to uncheck the "show photos in subfolders".
Thanks for the reply and suggestions. I do need to make .jpg's to send to my agencies for the initial selection then I can delete them afterwards. I'll try not using the sub-folders but since I have to do a "Save As" in PS since I have to add my initials on the .psd and the .jpg it seemed a better way of sorting things. I originally imported these files and sub-folder LR, which was a mistake perhaps.
I just need to better get my head wrapped around what LR is doing and how to use the Filters and perhaps Collections better.
Thanks for the reply and suggestions!
It came down to more of ticking off the "Show Photos in Sub-Folders" option. Still work to be done on the best workflow. I do need to create a .psd and a .jpg, the .jpg file required for the agencies initial edit. Of course after that selection is made those can be deleted and the .psd, with adjustment layers, can be sent to them.
Personally, I find it much simpler to work with a single folder and stack different image types. I can have my original NEF file, and a TIF file, as well as a soft proof virtual copy. I stack those, and only display one image normally. He keeps everything together in one folder, and for me is very easy to handle. But then, I'm not a professional photographer. My system might be far too simple.