Just some way to recognise that a boss battle is happening. At the moment I tend to have arrays that I pull from to determine who the enemy is. You could have a variable that is normally set to -1 (ie random battles) and you set that variable to a particular number when you want to fight a particular monster.
This means you just need to keep resetting that variable to -1 at the end of a battle.
How/when you set that variable to something other than -1 depends on how you have your game setup atm.