"The player executes the order and then places the token in the “Special Order Pool” of his Faction Sheet. He may only choose this option if the number of orders in his “Special Order Pool” is less than the number allowed by modules and strategic areas he controls."

Does that mean that if I have two R&D modules, for example, I can only execute one special order?

Nope, since the number in the pool is checked before you add the new token.

ok thx