The file's ~/.bash_profile, ~/.profile, or ~/.bashrc. It'd probably be best to put it in ~/.bashrc, because that's the script that gets executed every time the shell starts (AFAIK -- you might have to put it into the other one, too, though), while .profile and .bash_profile only get executed when you first log in.
~ is a shortcut for "my home directory", or /home/<user name here>.
But I'm curious, why make an alias out of these? The line you've posted (alias export __GL_FSAA_MODE=2) isn't even really valid syntax (the alias command requires an equal sign, like alias l="ls --color=auto -F"
, like I have in my .bash_profile), but even with that in there, the variable-set wouldn't happen until you typed in the stuff on the left side of the equal sign, When I do an l, the output of ls comes up in color, but not every time I log in.
I would think, at first, that it'd be easier to just do the export, without the alias, and let it just set that environment variable for the whole time the shell is running... but maybe not. Just wondering about the reasoning...