I'm not familiar with csh shell, but with Bash for example, when you add something to .bashrc or any other such file that your shell reads, the effect will be there as of the next time you start that shell, either by opening a terminal, or whatever.
When adding something like an alias to the /etc/profile file, it will only be in effect after you source that file, OR it will be in effect system-wide, after the next reboot (or perhaps going to init 1 and back to init 2/3/4/5 will work also).
When adding stuff to the dot-files in your $HOME directory, it will only work if you're sure that your shell actually READS those files when it is invoked.
For example, Bash reads .bashrc and maybe .bash_profile when it is invoked; therefore, if I were to create a file called .profile in my $HOME, I would need to make sure that either .bashrc or /etc/profile had a line that sources my personal .profile file.
The same idea applies with csh or any shell: if you add things, like aliases, to some file such as ~/.profile, you need to make sure that when csh is invoked, *something* is telling it to read your .profile file, so your additions will be read.
Hope this helps a bit.
PS - it may differ for your system, but on my Slackware system, the alias for `ls` is in /etc/profile, so it becomes active for all users, as soon as the machine is booted up.