Do I need to separate all the eggs if a recipe needs more yolks than whole eggs? I am going to make lemon bars except I am going to use oranges instead, so I was reading the recipe for lemon bars. 

The recipe calls for 2 large eggs and 1 large egg yolk separated, then in the instructions it says to beat eggs and egg yolks together in a bowl. 

Wouldn't it be okay to just leave them as whole eggs if they are going to be mixed together anyway?
Your recipe calls for both whole eggs and egg yolks. (Presumably, it needs the extra fat from an additional egg yolk without the liquid/protein contribution of an additional egg white.)

Since the goal in this recipe is just to have 2 whites and 3 yolks in the mixture, there is no reason to separate the first two eggs. So you will only need to separate one egg to get that extra yolk.