As far as orientation, I'm sure you've read to use the rear fans to expel air and the forward fans as intake. This is correct. Air cooling is based on the ability to bring air in, heat it, and get it out of the case before it can transfer that heat to anything else. Typically, this means bring your air in from the front and bottom, and expel it through the back and top. If you ever have a side fan, this fan's orientation should based on your other cooling.
If you can manage your CPU fan(s) using the onboard headers, do so. This keeps your CPU cooling independent of the rest of the machine, allows your motherboard to power-manage for optimum power usage and fan speed/noise, and gives you manual control of fan speeds on the motherboard BIOS if you so choose. I'm seeing your choice in fans is indeed PWM, so that's the route I'd go. If you have only one header, connect both CPU fans to it via the chain connector on the included cable. Otherwise, use all of the headers available.
Similarly, use the motherboard case fan headers. Use one for the front and one for one or both of the rear via their daisy-chain connection.
In PWM setups, it's common for only the first fan in a chained set to be monitored by your motherboard. It's usually a safe assumption that they are moving at the same speed, and both will have their power varied by the motherboard, but be aware of it. That's why you want the fans on different headers; maximum clean power flow, monitoring, and control while separating concerns based on what the fan is actually doing.
What you don't want to do is connect any of the fans using a 4-pin molex -> PWM adapter. You would only do this if you wanted to a) use your PSU's power rail to directly power the fan or b) hook it up to a fan controller. In the case of the latter, most fan controllers are garbage and trend to an early death or bad ports. In the case of the former, this puts more strain on your PSU, and the more things you connect this way, the more PSU rails you have to take up. Your PC is a normal desktop size, so this is less of a concern compared to my 30-fan dual case, but you'd also lose the ability to control the fan speed (unless you got one of those fan controllers I just warned about).
I wouldn't put more than 2 fans in a PWM chain. I did this once and found the mobo started sending insufficient power to all three fans because it was just sending enough juice to power one of them properly.