I just create thumbnails the correct size right off the bat. I don't ask X-Cart to do any resizing. So if my thumbnail width is set to '100' then I make all my thumbnails in Fireworks (using the batch feature) to a width of 100 pixels.
X-Cart by default stores thumbnails, category images and detailed product images in different tables in the database or if you are keeping your images in the filestsystem they are named differently so you can distinguish between them when thay all live in the same directory.
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