Couple tips: Try to get higher combos for money, if the zone you are in has a boss (danger level will be upwards of 7000) get the boss low then enrage kill him for double the money. Also clearing a zone down to zero danger prevents the danger level from rising again (and thus always get full money from your factories). Finally the different tower types only change how they handle in the assault missions (they don't change how much they decrease the danger %) so feel free to upgrade them to level three.