Questions questions on how to back out of duplicates not on Iphoto,

I have had my macbook pro 3 yrs and keep it updated. I was mistrustful of Iphoto as it did not seem easy to organize photos the way I wanted so I have loaded all my photos to a file in my document folder. Now I have what I am being told is nearly 15,000 photos and I have a lot of duplicates in my files OFF of IPhoto. I think tho that they are eating up my storage as it's very low and things seem slow esp Iphoto and some other stuff (like this site).
I have finished grouping them in the separated files the way I want, which is topically, and except for a very small group which I renamed but left the numbers, they all have original numbers. In some cases I have 3 copies in different folders or rolls OFF of IPhoto. The ones on IPhoto are complete as I have used Iphoto cautiously.
I was going to delete duplicaes off the hard drive (remember they were never put on IPhoto at least by me) until I read all those cautions about deleting and have to tell you I started to delete duplicates by hand off the hard drive (selecting one of two same numbers and kept 99% of the ones marked "orig" and nothing I did has effected the Iphoto as far as I can tell--the numbered pictures show up, but there are a handful which I can see don't have the "ORIG" on the name but still show up in the library anyway...and all of them have JPEG bec I found that was the easiest way to get them on. So far dumb luck.
Now I'm afraid to delete the harddrive duplicates even tho they were not put into the Iphoto library by me manually. It does appear that some of the folder names I have used are there, some have complete sets and some have no photos in them at all, can't remember how they got there.
I am now ready to send the organized photos to IPHOTO (after making a backup) but I'd prefer to eliminate duplicates on the hard drive folders first. Remember, I loaded these into my documents folder and not into IPhoto to begin with.
Can I do this and should I eliminate only files that don't say "ORIG"? Will I have to buy software to eliminate duplicates on the harddrive folders I made? Plus, they are duplicates mostly bec I like to have a copy of the original roll, and the original set, and then my subject matter files (sort of cross referenced). As you can tell I am not willing to give up control over the photos on how they are arranged. Still Iphoto is a lot easier to look at them and edit them if necessary.
I have an Olympus with a memory card and have learned I can name the download before importing them, but there does not seem to be a easy way to separate them into different groups and Iphoto isn't the easiest to do this beforehand either. Can you tell me a easy way--it seems it must be through the View, can I select this when I choose a download preference and name the download group? I don't like a default download bec then you always have to move them. Any suggestions?

1. If deleting photos off Finder messes up Iphoto files, at what point is the connection between the harddrive file and the Iphoto file made?
When it's imported.
Do I have to choose the connection or does the system do it automatically?' Because if they are connected and I delete don't all these dire warnings apply?
Read the above: If it's a Managed Library...
2. When I have done downloads, they happend pretty automatically and don't give me a choice of identifying files with keywords or anything else, it's more like a dump. I am used to putting new material in a specific file and not having to rearrange them after they dump into Iphoto. So how/where do I control the naming and grouping of items before I put them into Iphoto? Iphoto is like shuffling cards after they've fallen it seems...
Perhaps you should look at the tutorials
3. Users should stop saying how great Iphoto is if it can't be simply explained how the two groups of data inter relate. I am not going to use a library system if I don't understand how they interrelate and one of the earlier posts basically said this info was proprietary.....
You don't get to decide what Users say or don't say. If you don't want to use a Library system then don't use a database for your photos. I will say this tho': people with even very rudimentary computer skills seem to be able to grasp the concepts.
None of the metadata that you add in iPhoto is proprietary, with the possible exception of Faces, and that's only because there is no agreed way to share this info in any application. All Faces data is proprietary in all apps that offer the feature. Anything else you add - keywords, captions, titles, location etc can all be written to the file on export from iPhoto.
As to you comments on keywords: They are not a replacement for Captions, Titles and so on, they are an addition to them that add greater flexibility. For instance, if you have a photo of your Dog and a Tree, what category does it belong in? The Dog category? The Tree category? With keywording and a couple of really easy Smart Albums the same photo can be in both.
As to the granularity of your keywording system: that's up to you.
Regards
TD

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