There are a couple of things about iPhoto that a lot of new users don't 'get' immediately. Perhaps this will help.
First, iPhoto is a Digital Asset Manager (DAM) - along with Aperture and Lightroom and, sort of - Capture One. One of the things that DAMs have in common is that they are designed to organize your images, and also to edit them. That is... they assume that you will be accessing your images exclusively through the DAM interface and not through the Finder (there are some exceptions - but I'll keep it simple).
So... if you are accessing your photos through the Finder (you don't say whether or not you are, but I suspect you are) then that is the first problem.
One of the other things common to a DAM is that they are databases. Part of what gets recorded in the database are the metatarsi - like keywords, ratings, flags, etc. etc. More importantly - they also record in the database a record of what you do in the say of edits. This is really important: When you edit the image in a DAM the original image is not altered at all... it stays untouched and safe. This is called 'non-destructive editing' (vs an editor like Photoshop or Pixelmator which create 'destructive edits').
I am making some assumptions - based on my experience with new users of iPhoto. (If I'm wrong - please forgive me). But it sounds like you are trying to organize your photos via the Finder and going into the Library package via the backdoor, and expecting to see the edited versions there. Or that you have set up iPhoto not using the default installation settings... something like that. Because it sounds like you are seeing the original version of your photos and not the version that has been saved by (and into) the iPhoto Library (database).
If you have been accessing and moving etc. your photos via the Finder and not through the iPhoto interface then you may have corrupted the iPhoto database. Which shouldn't bork the entire collection... just the images that have been affected. Without seeing the library it is impossible to tell how to put it all back together again.
Anyway... there is a lot of good info in this forum... do a search on DAMs and you'll find some good threads.
Hope this helps.