Hi,
I think your needs are similar to mine, mentioned in "Viewing folders" thread earlier (see 3 last posts).
What I did -- just switched to "Folders" view, selected a folder, then -- all the photos of that folder, and "moved".
It's a bit uncomfortable now for changing location of huge amount of files, as only photos can be moved, not the whole tree structure of folders at once (so you have to do "select->move" folder by folder), but it works. And I believe Asaf will do something more comfortable some day 
Guoda