Program to help orgnize photos? Particularly save over duplicates?

I have thousands of photos stored on my computer and on an external hard drive. I know that several are duplicates. I am trying to re-ogranize and delete things but am finding it difficult because when I go to move images into a folder to sort it, if it sees a duplicate, it doesn't ask if I want to override, it just does not do the job. It will be very difficult for me to use the thumbnails to see which of the thousands of images I have are the duplicates. I hope this is making sense. Maybe I should elaborate.

I am trying to organize my files by location. Lets say I already moved 1000 images into a folder labeled "DC". I now want to copy 1000 more (some that may be duplicates). It wont let me copy because it says there are several duplicates but it wont give me the option to save over it like windows used to. This makes it very hard to organize.

Is there a program or application that will make my job easier? I've tried Xfolders and mucommander but they dont let me see thumbnails, that makes it much harder.

iPhoto will automatically prevent duplicates from being imported, alerting you when you attempt it.

Thanks for your quick reply. What I am trying to do is organize thousands of photos that I have on my harddrive and my external. If I organize them into iphoto, how will that help the organization? Will I be able to export them all out in an organized catalog?