I struggle with this. I use iPhoto because that's what everyone else in my family uses so I can easily upload pics to my Mobile Me gallery and others can subscribe to the pics in their iPhoto programs. I upload to iPhoto, tag, delete, organize, etc. If they are pics that I'm not doing anything with, I do some minor editing in iPhoto and that's where they stay.
If they are portraits or other pictures that I want to use in LR or Photoshop to make some major edits then I export them to a folder and then import from there into LR and PS to make my edits.
It's kind of complicated, and I'm not sure it's the most efficient way, but it is what has worked for me so far.
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