Hey guys I have been working on a boss zombie recently and used some of this tutorial found here: http://www.zombiemodding.com/index.php?topic=4099.0
It works alright I changed it a little but the one issue that I cant figure out is how to disable points when you shoot the boss. I've tried adding a check in zombie_damage() and zombie_damage_ads() in zombiemode_spawner.gsc but I cant figure out a way to write it. Every time I try to add a check it just disables points for all zombies. Is there a way I can set some kind of variable for the boss so only he doesn't have points?
This is one example of what I tried which takes all points away:

if(level.boss == true)  // I need some kind of variable here
{
        set_zombie_var( "zombie_score_kill", 				0 );
	set_zombie_var( "zombie_score_damage", 				0 );
	set_zombie_var( "zombie_score_bonus_melee", 		0 );
	set_zombie_var( "zombie_score_bonus_head", 			0 );
	set_zombie_var( "zombie_score_bonus_neck", 			0 );
	set_zombie_var( "zombie_score_bonus_torso", 		0 );
	set_zombie_var( "zombie_score_bonus_burn", 			0 );

}

Any help would be appreciated.

Majority(if not all) of the scoring logic is handled in _zombiemode_score.gsc. I wouldn't know exactly what you would need to change because i've never made a boss zombie before or seen the script that your making so yeah. 

If nothing else you could (probably) take the points away as the player receives them, but it'd look real stupid. lol

Your logic is incorrect. You are looking at the wrong place to take over the score values. Looking at your example it is very clear why you are only able to change the points for all zombies and not just the boss.

In _zombiemode_spawner there is a function which handles the damage the zombies recieve from players. What you need is a .variable on the boss zombie (set it when he spawns) so that you can do a check similarly to:

if(!self.boss_zombie)

where self is the zombie ent in the damage function. Add your logic for this bool to the zombie_spawn_init() function in _zombiemode_spawner. All non-boss zombies should be set to false.

As far as where to put the check, look at the first ~20 lines of zombie_damage() in _zombiemode_spawner.

Adding the above logic to the existing code, it should look like this:

if( self zombie_flame_damage( mod, player ) )
	{
		if( self zombie_give_flame_damage_points() )
		{
			if(isDefined(self.boss_zombie) && !self.boss_zombie)
				player maps\_zombiemode_score::player_add_points( "damage", mod, hit_location, self enemy_is_dog() );
		}
	}
	else if( self maps\_zombiemode_tesla::is_tesla_damage( mod ) )
	{
		self maps\_zombiemode_tesla::tesla_damage_init( hit_location, hit_origin, player );
		return;
	}
	else
	{
		if(isDefined(self.boss_zombie) && !self.boss_zombie)
			player maps\_zombiemode_score::player_add_points( "damage", mod, hit_location, self enemy_is_dog() );
	}

If you have a tesla gun in your map you will need to handle that as well.

Majority(if not all) of the scoring logic is handled in _zombiemode_score.gsc. I wouldn't know exactly what you would need to change because i've never made a boss zombie before or seen the script that your making so yeah. 

If nothing else you could (probably) take the points away as the player receives them, but it'd look real stupid. lol

Both of your suggestions would be handling the problem after-the-fact, which by definition is not the way to go about preventing something.

None of the scoring logic that he would need is handled in that file. That file handles the scores that the scripts have already determined should be given - it should not be responsible for checking the validity of incoming scores. If you don't want a score to happen, don't call the score function. Simple as that.