Applications-Won't let me remove photos that should not be there

I was moving 6000 photos from an external HD onto my laptop so I could organize them in iPhoto 08. I'm still not exactly sure how that process should go because I have had several issues.
1. Many of the photos "could not be found." iPhoto would say "do you want to find photo?" I would have to exit out of iPhoto library to get it to unfreeze from this state. When I went to open iPhoto again I would have to go into Applications and click an iPhoto Applications Folder icon to get the iPhoto library again. I could only find iPhoto Library icon in weird places and there were two of them. When I clicked "Get info" I knew they were two different ones because one would say 8.3Gigs and the other would say 300KB (this seemed too small to even have photos in it), but both were iPhoto 08.
2. As I was transferring portions of my photos from the external HD I accidentalIy clicked on the Applications folder. Even though I tried to stop it in the middle it copied almost all of the 6000 into A. Applications B. iPhoto 08 (with many problems), C. Pictures which I had set it to do without keeping a backup copy of originals and D. Nikon View with MANY duplicates.
After that I went back to delete the ones from applications and it tells me " Some of the items you are moving are in use by another application. Moving the items can cause problems with the application using them. Are you sure you want to move these items.
(Maybe this somehow correlates with the fact that I have to open the iPhoto Library from an Application icon every time I turn on the computer? Didn't have this problem before I updated to iPhoto 08).
Tracy

I couldn't get them to copy until I put them on my computer -at least that is what I remember
1. Verified HD. This is what it said.
Verifying volume “My Book”
** /dev/disk1s1
** Phase 1 - Read FAT
** Phase 2 - Check Cluster Chains
** Phase 3 - Checking Directories
** Phase 4 - Checking for Lost Files
91324 files, 2676672 free (7947966 clusters)
Mounting Disk
2. What do you mean "get the Applications moved back out? I still have thousands of photos in my applications

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Applications-Won't let me remove photos that should not be there

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