Besides dragging 'n dropping files between the two file windows, you can also drag files from outside (e.g. from some windows explorer window) onto the remote dir to upload them.
However, you can't drag files from remove (ftp) to outside FlashFXP, e.g. to an explorer window, to download them to that dir. You have to go there inside FlashFXP in the local fileview, and then drag it.
Would be great if you add dragging 'n dropping files outside FlashFXP too!