Personally, I consider my LR library only a place for my originals. Be they RAW, JPEG, or TIFFs of scans I’ve made. They all get brought into LR, tagged as much as possible, and processed.

If processing is done outside of LR, I will bring this edited image back into my library (unless automatically done so by some plugin) as a separate instance and therefore a completely separate original. So, now I have two copies of my original, it’s just that one is processed differently. I think of this in the same way I create a “virtual copy” or “snapshot” in LR directly.

As far as images that I explicitly use the “export” command for, I have gone the route that any exported image is destined for something other than my local file storage because that’s what I have LR for…I can always re-export images and do so all the time. Yay for export presets!

Once the exported image is sent where it needs to be (e.g. 500px, G+, Flickr, etc.) it promptly gets deleted from my hard drive!

Lastly, I have made sure that my default export folder configured in LR is a place that resides at the root level of my LR library folder. For example, my storage structure is:

Image Vault (root folder)

------ Image Exports

------ 2010

------------ Mt. Everest

------ 2011

------------ Bot Gardens

------------ Family

------ 2012

------------ Bot Gardens

----------- Landscapes

This way, I know that my backup procedures will capture anything within the exports folder in case I don’t have time to upload images from here and suffer a hardware failure.

Edit: I don’t use the feature in LR for exporting directly to places like Flickr because I’ve found it to be slow, unreliable, and doesn’t give me the level of control I want. This is just my personal preference and I believe others can utilize this feature with success.