All three (3) items that you mention have been documented elsewhere in this forum. The ability to create Collections on removable media seems to be the biggest heartache for most people.
As for the organization of the MS/SD, the Sony software displays all files as one flat directory even though it may be split into multiple subdirectories on the media. Since I load the mp3 files outside the Reader (at USB 2.0 speed, not USB 1.1) I place them in their own directory as they change more often than the books.
For basic organization, I am using the main memory for books. (While I was promised 64 MB of storage the CONNECT software reports 91.9 MB total space.) The removable media contains mp3 and jpg files, each in their own directory and each loaded outside of the CONNECT software.
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