same here, i just installed in manually.
create a new server and make note of the name,
download the server files for the new direwolf pack and put them in the directory of the server that you made. it will be the same name as the server.
it should show up on the dashboard and server list.
i use winscp to ftp into my server.
the directory will be under /var/games/minecraft/servers/servername
the other option is to put the linux server install file in that directory, make it executable with chmod +x and then run it from the command line with ./filename i always do the server maint under root but you can also use the basic admin acct for the web admin page and use sudo in front of the commands
i know enough linux to get me in trouble, so if any of you linux gurus have any corrections to my suggestions, they are welcomed