"if you use rapget, this method will not work so effectively as the program does not preserve target destinations for downloads in queue the way that a real download manager like Flashget will"
There is a workaround for this problem.
After the files are in the queue, select the ones to go in a chosen folder.
Right click one of them.
Select Change.
Write in the correct folder. Only the selected files will go to the new folder.
