In my case my mobo has 3 fan headers (in addition to the pwr header and 2 cpu fan headers), the fans themselves are from noctua and come with 4-pin connectors and a y-cable (4-pin + 3-pin into a 4-pin). There's also an extension cable (4-pin) with each fan.
Would it be okey to just tie them all together with the y-cables then wire everything (as in all of them) into the most convenient case fan header? (2 of the case headers are kind of inconveniently placed in the middle)
Be careful using the Y cable with the motherboard fan headers. It may be OK or it may not be. There are two reasons not to do this. One is, the fan header is designed to provide a certain amount of current. It may be time to start learning about current draw and power requirements? This is the kind of thing that depends highly on your exact motherboard, so only you can answer your question.
Second, there is usually a microchip that can sense and control fan speed for you, and it can set different fans to different speeds. In principle it's nice to have precise control over each fan.
The usual way to hook up extra fans is to wire them to 5 V or 12 V from your power supply. You may have received a voltage-reducer in the Noctua stuff. You won't get computer control of those fans but at least you'll be safe power-wise. You'll need a molex-to-fanheader adapter.
The better cases have a small fan controller that let you hook extra fans to it and control them manually.
Yeah I've read that apparently in general you can only really assume 1amp per header, and a fan can take up to .5amps but noctua supposedly might go a little higher so it's probably not safe to put two on the same header since motherboards dont really protect the headers in any way (or so people are saying).
I assume using the extra CPU fan header is an option (since I'm not using it), is it possible to use the pwr_fan header when available? since PSUs don't seem to have anything special with regard to fans (and mine doesn't appear to have the sensor required for it anyway).
My guess is that using the 2nd CPU fan header is fine, it will likely run a little faster. Check your motherboard's user manual just in case it has some info on that header. I don't even know for sure if they include that information.
Yes if you connect to the power supply you have to figure out where 12 V or 5 V is, find/make an adapter to the fan plug, and maybe use a series resistor to bring down the voltage a little and run the fan around 1000 RPM. And there is no sensor, just power and ground.