Should the cool side small fan drive the air on the peltier or away from it. What should I do, maybe place a larger fan on top to drive air away from the cool radiator and into the box?

What you need to do is circulate air between the Peltier cool side and the volume of the box. It doesn't matter whether the fan is moving air from cooler to box, or the other direction, as long as you have a return air path to circulate the air around without it leaving the interior of the box.

Can I control the peltier temperature with pwm, as I do with the fans, or will i end up burning the unit. I should mention that I control the pwm with two mosfets (tip220) to drive the max 12v to the fans.

Fast PWM (many Hz or quicker) is inefficient, but doesn't damage the Peltiers. Linear control is better. Slow PWM (or on/off control) is both inefficient and will damage the Peltier module.

The difference between fast and slow is whether the temperature of the Peltier follows the on/off cycle of the PWM. Peltiers have a wear-out mechanism whereby repeated temperature changes can de-bond the elements from the top and bottom plates.

The difference between PWM and linear control is the fact that the heat generated in the Peltier is proportional to current squared, whereas the heat shifted into the cold side is only proportional to current. Turning the current on and off (ie PWM) generates more heat for the heat shifted than does a steady current of the right magnitude.

Should the cool side small fan drive the air on the peltier or away from it. What should I do, maybe place a larger fan on top to drive air away from the cool radiator and into the box?

What you need to do is circulate air between the Peltier cool side and the volume of the box. It doesn't matter whether the fan is moving air from cooler to box, or the other direction, as long as you have a return air path to circulate the air around without it leaving the interior of the box.

Can I control the peltier temperature with pwm, as I do with the fans, or will i end up burning the unit. I should mention that I control the pwm with two mosfets (tip220) to drive the max 12v to the fans.

Fast PWM (many Hz or quicker) is inefficient, but doesn't damage the Peltiers. Steady current of the right level is far better. Slow PWM (or on/off control) is both inefficient and will damage the Peltier module.

The difference between fast and slow is whether the temperature of the Peltier follows the on/off cycle of the PWM. Peltiers have a wear-out mechanism whereby repeated temperature changes can de-bond the elements from the top and bottom plates.

The difference between PWM and steady current is the fact that the heat generated in the Peltier is proportional to current squared, whereas the heat shifted into the cold side is only proportional to current. Turning the current on and off (ie PWM) generates more heat for the heat shifted than does a steady current of the right magnitude.