This is a great question - kinda on par with which came first, the chicken or the egg.
Here's my opinion:
I would load first and organize second. The main reason is because with all the wonderful plug-ins that have been created, it really makes organizing the books once loaded, so much easier.
I have been using Calibre for about a year and half and seen the unbelievable development of this program for a while and can tell you I wish that half of what you can do with Calibre today had been there when I started out.
Plus, there are a ton of very nice people here to help you along the way. I probably would not have been able to figure out much of this stuff had it not been for some very patient people. Either way you can't go wrong. Good Luck!
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