Hello,
1. the ports dont matter as long as you connect the first port on the one side with the "DOT" on it. Also, if you are using fans on that side and want PWM control, you have to connect the PWM cable to it for each side and then control in the bios. Each side will all be the same yes. I dont think asus has a sequence mode on theirs that I saw, but I know we have it with our TT RGB Plus software so should not be an issue.
2. You can connect the Pump LED to anything, shouldn't matter. If you dont have any fans connected either to that side, you dont have to use the PWM, it will only work for fans. Speeds and settings for the LEDs are set in the MB software, it is not a physical connection or control off the sync controller.
Should be fine to use the second controller for just the pump header LED, gives you some room as well for add ons later like some LED strips. I would also suggest if you can avoid putting all the load on one controller, split it up, but it still should not matter.
