Maybe this is not what you are looking for, but it could be a workaround.
1. Enable categories under the "Layout" button at the up right corner
2. Create a new Category, go to "Meta-Info" tab
3. "Open .torrent files created or moved this folder:" and select a folder.
4. Go to "Local Files" and set download/seed folders
From now on you just need to save the .torrent file to the right category's folder (Meta-Info tab) and it will be saved to the custom location (Local Files tab).
Also if you changed an existing transfer's category files will be moved to the category's folder (Local Files tab).
NOTE: There is a "Meta-Info" menu in general settings, make sure that the category doesn't monitors the same folder, otherwise the .torrent file might be deleted before the category could read it. (applies when "Delete file immediately after loading" is checked)