Couple problems with the 3 top fans with alternating Intake>Exhaust>Intake. Hot air is just exhausted and cycled right back in plus it messes up the overall airflow. It's preferable to have air flow in one direction within the case.
And I realize that the H50 instructions are for the fan/rad to be installed as intake but there's an example where the fans were reversed and actually gave better performance (
Corsair Hydro Series H50 CPU Water Cooling Kit Review - Results, and a "What If" Scenario - Legit Reviews). Granted the fans used for exhaust weren't stock fans but it's worth noting regardless. I'd go for something like:
Fan1: Exhaust
Fan2: disable
Fan3: Intake
Fan4: Exhaust (H50)
Fan5: Intake (KamaBay)
Fan6: Intake
That will give a bit more of a positive pressure.
For negative pressure you can try:
Fan1: Exhaust
Fan2: Exhaust
Fan3: disable
Fan4: Exhaust (H50)
Fan5: Intake
Fan6: Intake
And if you're sticking to H50 instructions with the fan at intake:
Fan1: Exhaust
Fan2: Exhaust
Fan3: Disable
Fan4: Intake (H50)
Fan5: Intake
Fan6: Intake
(fan3 disabled to prevent cool air from fan5 being exhausted prematurely)
In the first 2examples air is either being intaked from the front/front bottom/front top and exhausted to the rear/rear top.
In last config, cool air comes in thru front and rear and exhausted to the top.
Also since there'll be one fan unused, I'd put it at the fan holder at the drive cage just behind fan 6 (in same direction as fan6). It'll help with airflow as the interior of the ATCS 840 is really big and dead air areas can be a problem.