My guess (and this is just a guess) is that the motherboard's BIOS instructs the motherboard to supply a full 12V to the fan when the CPU temperature is above 72 degC. When the CPU temp is below 72 degC, less voltage is supplied.
If you have a spare fan with a 3-pin connector and also a 3-pin/4-pin converter, here is something you may try. First, take the Presario's CPU fan and plug it into a "normal" power connector with the 3-pin/4-pin converter. This is to make sure the CPU fan keeps running. Next, take another fan with a 3-pin connector (like an old CPU fan) and connect it to the CPU_FAN header. (Do not bother attaching this spare fan to anything. The only purpose of this exercise is to make sure that aftermarket fans will actually work at all on this motherboard.)
Now turn the computer on. If the computer boots up normally, then you should be OK installing an aftermarket fan.
By the way, does the computer show any sort of data about the CPU fan's RPM?
I don't know about the "total n00b" part. From the questions you are asking, it sounds like you have a pretty good idea of what is going on.