Importing and organizing photo files lightroom 5 for the first time. Clean up hard drive photo files

I have a trial version of lightroom 5 and would like once and forall to bring some order to both my hard drives and lightroom 5 collection. Some photos in lightroom 5 seem to have lost their path. some are in Window 7 folders and others are in Elements 9. I have made back up copies of some folders and would like to have a more systematic approach to back them up from now on. I have a NAS (network access storage) device and an extra hard drive I thought it would be best to use my laptop as the primary working memory for my photo files as it would be faster than working with the NAS or external, and then back everything up to the NAS and external. I see the main challenge as  consolidating all of the files and whereever possible preserving the ratings I have given photos; I would like to eliminate duplicats. on both the hard drive and in lightroom. i have looked at one of the initial training vidios on the 'library' section of adobe help and the presenter talked of two methods of importing photos,. the first and the one I think I will use going forward is to open lightroom and import from the sd card directly as opposed to having Windows 7 import and then having lightroom find them. If someone kows of a comprehensive list of instructions to follow to clean up my hard drives that would be extremly helpful? Peter

I doubt there is a list of instructions to clean up a hard drive, because every starting sitaution is different, and your "clean" is probably a lot different than my "clean".
But let's clear up a few things first. Based on your writing, it seems like you think you have photos stored in PSE and photos stored in LR. This is not correct. Neither of these programs store your photos. All of your photos are on your hard disk, in folders, somewhere.
With regards to missing photos in Lightroom, when you move or rename photos and folders OUTSIDE of Lightroom, Lightroom no longer knows where they are, and reports them as missing. To fix it, see: http://www.computer-darkroom.com/lr2_find_folder/find-folder.htm Related to this, you don't want to "clean up" things in Windows and also "clean things" up in Lightroom. Instead, once you import photos into Lightroom, you should do all photo management in Lightroom, not Windows, otherwise you will just be creating more missing files.
With regards to duplicates, Lightroom has some tools to detect duplicates. It will try to prevent duplicates on import, and if you do manage to import duplicates, you can use the "AutoStack by Capture Time" to try to find additional duplicates. But if those don't work, then you're pretty much on your own.
With regards to putting photos on your laptop to work on them rather than your external HD, I think you will find that this provides a tiny fraction of a second improvement in speed which you may not even notice, which will be offset by the time you spend moving photos to somewhere else when you are done. So, just put the photos in their final destination folder on your external HD or NAS, and don't bother moving them to the internal HD.
Which brings up another point. Once you have accomplished this "clean up", your workflow should be to put the photos in one place, and then don't move them! (Exception: running out of space on disk, or moving to a new disk/computer) Make your life as simple as possible.
One last point: strongly consider using keywords and other metadata to achieve organization, instead of moving photos/folders from here to there to achieve organization. These tools in Lightroom give you ability to organize in much more powerful and flexible organization than anything you can do by moving photos/folders from here to there. (Side note: if you want all photos in some sort of centralized location because it meets your storage needs, then do that because it meets your storage needs. Within that collection of photos in a centralized location, use keywords and other metadata to achieve organization and for searching)

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