In future, pay attention to the Destination panel when you import. That's why stuff ends up in a certain place.
For the missing folders, right click a folder and choose Find Missing Folder. This prompts you to tell Lightroom where the folder is now located. If you fix a parent folder, its children will be fixed too.
Nik seems irrelevant to these problems. It's still good software. It just saves its files next to where you saved the originals.
I use Lightroom CC 2015, and I also use the Nik Plug-ins. When I send an image to one of the plug-ins Lightroom creates the TIF copy of my raw image and sends it to the plug-in. When I'm finished with the plug-in, the result is always saved to the image Lightroom created. It's always in the same folder as the original. Everything works as expected. My guess is that you probably are not paying close enough attention to where your images are imported. You are in control, so take control.
Jim, I'm gonna have to see exactly what I'm doing and dig deeper..... Still trying to get used to LR after Aperture 3 was killed off. All of my catalogs I've created upon Import are located on my external. Essentially creating individual folders for each of my shoots. Kind of frustrated, as in order to open up my catalog, I have to go to my external.... catalog opens and my images appear in LR, yet if I remove the folders on my main HD on my iMac, the photos cannot be located.... it's as if the files are being stored separately between the two drives. I guess I assumed if the catalog is created and placed on the external, all of the information would also be retained there as well. So am I just storing the catalog on the External, and the files I've been importing going to my main??? I miss Aperture... LOL
Keeping your photo files on an external drive is a good practice - however be sure to back up that external drive to another drive so you always have two copies of the originals.
I have found that by keeping my LR catalog on my internal main drive and the photo files on the external, LR does work a little more slowly. Using Smart Previews (with those previews on the internal main drive) does speed up some editing.
I also recommend maintaining a back up of the LR catalog on that external drive - fast way is to have LR create the back up on that external each time you close LR. That way when you back up the external drive onto another external drive, you will not only have a back up of the photo files, but also a back up of the LR catalog - and thus 2 copies of everything.
The location of your catalog and the location of your images are completely independent of each other.
Your catalog can be located on any local drive, internal or external.
The images can be located on any local drive or network drive.
The images are not "in" the catalog. They are on your hard drives just like your other data files. The images are referenced by Lightroom using the path and file names.
When you do an import, LR uses the location in the Destination panel to copy the picture to. By default, that location is your "pictures" folder on your internal drive (c: for windows users). Use the Destination panel to pick a different location, like your external drive.
For the images on your internal drive, use Finder to copy them to the external drive. Then in the Folder panel in the Library module, do a "find missing" or "relocate" or the like as needed to show the new location of the top-most folder you moved/copied.
Just to be sure we are on the same page, the catalog is a database. It is the only file that Lightroom opens and manages. Your images are imported into folders on your hard drive and a pointer to those images is added to the catalog. When you import you have complete control of where those images are placed if you are importing directly from the camera card. If you are importing images that are already on your hard drive you have the choice of simply adding them to the catalog where they are located, or you can choose to move them to a new location. All of this is set up and controlled in the import dialog. You might consider watching the following video: