First, 8888 is too high. The Game_Variables class maxes it out at 5000.
Second, it should be a double equal sign, like so:
if $game_variables[888] == 0
ATB_PARTY_COMMAND_WAIT = false
else
ATB_PARTY_COMMAND_WAIT = true
end
and []= is, in fact, a method. It is located in the Array, Table, and Hash classes, for instance, in addition to the Game_Switches and Game_Variables classes (which are really just wrappers for an array). It can be defined in any class, if there is a reason for it.