After about an hour of using winscp to muck around in my linux install, I have found it infinitely easier to just use the command line in Putty. With a few cheat sheets, it is so much easier to move things around and edit them. There are no clunky menus(Those are only any good if you can’t or don’t want to figure out how things actually work.), it is just simple as can be.
My only complaint is that I wish that the help docs and commands were a bit more uniform across tasks.