Using LR is very simple.
You take your memory card out of the camera and put it in a card reader (or connect the camera to your computer, Not Recommended IMHO) and use either LR or some other method, like Win/File Explorer/My Computer/Computer/This PC or Mac Finder, to COPY the images off the card/camera into a Folder of Your Choice. If you used LR to do that they also import them into the LR catalog, Database, file. If you used a File Manager as noted above then you Import them into LR.
Once imported you can edit them in LR then Send them, Edit In, Photoshop or some other image editing program of your choice. Where the new files are saved that are created by editing them in some image editing program is determined by the options You have Selected in the LR Export dialog window and in the External editing section of the LR preferences. Or if you chose to do a Save As in the external editor where you chose to save them (Note if you use the Save As function they will not be auto added to the LR catalog).
The organizing of your images is done by you. On what drive and in what folder, along with the folder name (options are limited when using LR to copy and import at the same time but can be expanded in certain ways) is a choice you make at time of import or before.
For images that are already on your drive you again sort them as you like, placing them on drives and in folder that you chose before you import them into LR using the OS's file manager. At least that is what I do.
Although there are many books on the using of LR I have found the Scott Kelby ones not to my liking. The Martin Evening books I like much better.
I suggest you start over by creating a New Catalog, File menu item, select New Catalog. Name whatever you like and place it wherever, on whatever drive, you like. Then sort your images into folder and sub-folder before you import them. Some people like to keep all images in one folder. I like to separate them into Years, Days with months. Top level folder is 2006 > 2015 with image placed in sub-folders named by the day and month, 0506> 0715. But you can do it any way you like.