say you have the gain for a sub set to the recommended rms @ 3/4 the volume. Now you use the equalizer and boost 50hz 9db or something. Now when you go up to 3/4 the volume, their is much more power going to the sub then what you had set the gains for, causing the sub to possibly be distorting (or amp clipping) at this point due to your equalizer settings.
Setting up your equalizer before setting the gains eliminates this problem.
Usually its better to decrement octaves on an equalizer then to increase them, in which case, if you do that, then you do not have to worry about setting the gains first.