So, the stock Fractal fans are pretty good, for stock fans that come with a case, but they are not really in the same conversation as any high end fan. Yes, there is a major difference in specifications between fans they "throw in for free" and fans you pay 25 bucks each for. Significant differences. So, no, not happy with stock fans, ever. I generally take the stock fans out of any build I do that has a case that comes with them and set them aside for adding to systems that only have one or two fans but could benefit from more, unless the owner of the case preferred to not upgrade the fans in which case I'd usually just add one or two more that matched the stock fans.
Three front intakes, one rear exhaust and one top-rear exhaust. That is the formula that works best for pretty much 99% of tower ATX cases when air cooling is being used for the CPU. You don't really want to use the middle or front fan locations on the top because it just tends to "steal" the cooler ambient airflow coming in from outside away and send it right back out those exhaust locations and you don't want to run any top locations as intake because it causes unnecessary noise. I say unnecessary, because noise is really all it does, since any air coming in there either gets pulled right back out the top-rear exhaust or simply creates turbulence with the front intake fans and creating air pockets.
I don't use software to control fans. Fans are best controlled on modern motherboards using the BIOS fan control utilities.