Using that splitter I linked to will enable all the fans connected to the PWM motherboard header to spin up and down in unison, so they will all be controlled together as a single unit. 2 different PWM headers will allow you to control 2 sets of fans independantly.
From what I gather of your build I don't think you'd need to have different case fans running at different speeds, so in theory you'd only need to link off 1 PWM header and you're all good. Link that to Speedfan and you're all set.
As far as the fans running at 600rpm, you've already linked to fans that will do it, but if you're looking at different fans then just look at the spec sheet for them. You will find that they will be PWM fans.
Don't get hung up on the speed of the fans though. I know you want silence, so look at decibel ratings. I've had 120mm Gentle Typhoons that run at 1300rpm and are silent. I've also had cheapo 140mm fans that ran slowly but were still noisy. Also bear in mind that slower fans mean moving less air. Yes, the bigger the fan then the more air they can shift at lower speeds, but it isn't as easy as just getting a low RPM fan and be done with it. Especially if you're looking to use lots of fans at once. You need to move the air through your passive coolers, so check that your choice of fan can actually move enough at low RPM.