Devil's Advocate
I lie. A lot. Honest!
Jen, If you get Calibre (free ebook database management software) on your PC and then download the books to your PC it can organise the works wonderfully and then upload them to your Kindle.
+1 on this. In fact, +2 million.
Calibre is an absolute must for anyone who has ebooks. Terrific software, it's completely free, easy to use, and does a tremendous job of tagging and editing metadata for ebooks.
In fact, the metadata abilities of Calibre puts its music equivalents like iTunes to shame.