I set up pics in folders on the desktop. All folders in one main folder.
I sync that main folder in iTunes. It keeps the subfolder name on the iPad and the pics remain in their subfolder.
The iPad supports folders (directories), but not nested folders (subdirectories). For example, I had these folders of photos on my WIN7 laptop:
C:\Japan/Kyoto
C:\Japan/Tokyo
C:\Japan/Hiroshima
C:\Motorcycles
C:\Colorado
When I synced my iPad, it created separate albums for motorcycles and Colorado, but it took the folders for Kyoto, Tokyo and Hiroshima and lumped them into one album called Japan. (This is genius?)
What I ended up doing was getting ridding of all my subdirectories:
C:\Kyoto
C:\Tokyo
C:\Hiroshima
C:\Motorcycles
C:\Colorado
That gave me individual directories for each album. Subdirectories may work when syncing the iPad with a Mac though.
Agree and familiar with what you are saying, but there is no way to create or add photos to existing folders/albums/etc. directly from a Camera Connection Kit import while working on the iPad directly.