This howto is for a gnome based desktop like ubuntu, feel free to add howtos for other OSs.
-Open nautilus and chose File -> Connect to Server
-Set everything up like this (change the bookmark name if you want)
-Click connect which will take you to this box.
-Enter the password, which is maps
and choose "Remember forever".
-Click connect and you will be in the right place to paste your pk3.
-The next time you want to do this simply click on the bookmark and it will take you straight there.