Actually, I don't think you'll be able to have the alias help you once you are connected. You can do some more at the command line when you log in, check the ftp man page, but I think you can specify your username with the -u option (ie. ftp somesite.edu -u my_username).
Once ftp starts prompting you for info (like your password) you are on your own.
A number of years ago, there was a tool called "expect" that could be used to script such interactive sessions, but there might be other (better?) ways to do this.
Update 1 .. can't find the -u option in the on line man pages ... I could have sworn this was available. Still a tool like expect should be able to help.
Update 2: have you considered using sftp instead? If you set it up correctly, you won't need to supply the password, and you can specify the user in the command line, e.g.,
sftp username@somesite.edu also, scp will let you copy files to/from other sites, again with the username specified and passoword not needed if properly set up before.