Where best to store photos

I recently migrated from PC to Mac and am delighted with the Mac experience. However, my photos now seem to be scattered in different places. If I look in the Finder, some are in the "Pictures" folder and others in the "My Photos" folder.
When I first migrated I used iPhoto but have since bought Aperture for the added functionality and flexibility. So my iPhoto library has now been imported/duplicated into Aperture.
All in all It's a right old mess and, I suspect, entirely my fault! My first question: is there an ideal central location in which to store and organise photos on a Mac - and from which they can be backed-up to a Time Machine? My second question is; how do I go about deleting/removing all the duplicate photos?

I don't know how aperture stores the photos, but I assume it is similar to iPhoto in that it imports them into a centralized location.
Your "My Photos" folder is not a Mac item. It likely came along with your transfer from your PC. The Pictures folder would be the normal folder to place them into if you don't want to use Aperture's method.

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