Disorganized library - help with how to clean up?

Hi guys,
My library is an absolute mess. I have up to five duplicates of a given file, each of which are somehow at different sizes, and all my 50GB of files are spread out over somewhere between 4-6 huge and horrendously disorganized primary folders. Its mostly the result of 3 years of general disorganization, and more so somehow from importing and exporting libraries back and forth between LR and Aperture when I had no idea what I was doing with either program. Then I cant make stacks or get much done at all because all these images are in totally different folders!
But, I have a free external hard drive that I can export and import back and forth to in order to get this mess under control. The question is, how should I do it? How do I export my entire library correctly?
I dont yet know the difference between catalogs, libraries, etc. It seems as though I should export my library to the other hard drive as copied files, erase the original ones, and then re-import the copied files from the hard drive, while making sure it doesnt import thumbnails, suspected duplicates, etc. but Im not confident enough with the program to do so yet!
If anyone could guide me a bit, Id very much appreciate.
Thanks!
Alec

Alec-
You're not alone! Many of us have had to, or are in the middle of, organizing ourselves! It's a DAM headache! DAM, by the way, referring to Digital Asset Management, a term you might want to research.
I would start by backing up and asking yourself how do you want your system to look in the long term: how you want your library structured, and, importantly, how you want your library backed up. If you can come up with a good plan, there's nothing wrong with starting "from scratch", creating a new structure and moving your files into that new structure. While you're at it, create a backup strategy using at the minimum an external hard drive and DVD's so that as you populate your system you also protect your files from a system crash. Hard drives and DVD burners are cheap these days, compared to losing ~50GB of images!
People take different approaches to structuring their file systems and their libraries: there is not a "best" way. The important thing to me is to set up my folders in a way that I can eliminate guess work as much as possible. But as I do this I also make plenty use of Lightroom's collections and keywords. My pictures get cross-referenced in this way so that I can find them from several directions.
With Lightroom, you can export and re-import, or you can move files and folders from one location or disk to another. With your free hard drive, once you settle on a long-term file structure, you need a way to "point" LR to your new drive: try right-clicking on an existing folder and choosing Show in Explorer, then cutting and pasting it into the new drive and file system. When you close the explorer the folder in LR should show up in red as missing; you then right-click the folder and choose the option to locate the missing folder, then navigate to your new location.
Lightroom doesn't have a way of managing duplicates. If you try to import a duplicate it by default declines, although you can tell it to show them in the library anyway. If you have duplicates on your system you have to come up with your own method of finding them and dealing with them. If you have edited versions of a file, though, Lightroom can manage them.
Hope some of this helps,
Tony

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