I have 3x80mm fans, 2 of them are having larger rpm and airflow. In my case I have 3 places to install fan, 1 at the back of the case of exhaust, and 1 at the front pannel for intake air and 1 at the case cover for intake air to cpu/motherboard.
How do you suggest the locations for these 3 fans in order to have better airflow for the whole system?
I would use the weaker fan in front for intake, and use the other 2 for exhaust. Having the stronger fans on exhaust duty will both create negative pressure inside the case, so air will be sucked in from any available crack, gap, opening, ect. More hot air will leave the case and more cold will be sucked in.
your PSU will most likely be a 120mm that's exhausting hot air too.
its not like its hard to change fans around, so you should just play with all the various setups to see which is the best for your situation. personally, id start with a strong intake and a strong exhaust and leave the weak one out of the lineup.
experiment around and see what works best. I would put one of the more powerful ones at the front as an intake, the other powerful one at the back as an exhaust, and the less powerful one in the side as an exhaust.
Fan placement depends upon which are the hotter zones in your system, and which intake or exhaust areas have the most impedance to airflow. For example, a HDD rack with 3 drives butted up against an intake fan on the front is more likely to need a higher RPM fan, and the same is true if that case intake area (or the front bezel holes/slits/etc) in front of it has a crude stamped-out fan grill instead of a larger opening.
How about the video card? If it's a super-hot-running part and still valuable by today's standards, it makes sense to devote more airflow to it, at least the middling speed fan. However, there is a good argument to be made for negative pressurization, as the difference in real pressure is not enough to effect cooling by virtue of air pressue itself, but to have air sucked in through every available crack, opening, etc, is actually a good thing to eliminate dead spots, except that with "some" optical drives and floppies, it can fill them with dust.
You're going to have the case filled with dust anyway though, to a certain extent, unless the case is both positive pressurized AND all intake fans have a well-sealing intake filter, which will substantially decrease the amount of airflow through the system (by over 50% if the filters are dense enough to do much good, unless the filter panel area is several times larger than the fan intake area, and of course a slight distance away from the fan so it can pull through that larger filter area without another impedance of flow vs channel area.
If you have more than one HDD, I would not put the weakest fan in the front. If your video card is the most expensive part, I'd not put the weakest fan in the side. If your system is merely average but highly o'c CPU, you'd want the strongest fan in the back.
The side fan should usually suck into the case. If you put the strongest fan on the side panel, do not put the weakest on the front as it will decrease airflow past HDD(s) too much.
Now after all that, it may not matter much. When the case is pressurized (positively or negatively), it is not a large degree of pressurization, you'll ultimately still have most of the airflow in and out and at a fairly similar rate regardless of which fans are where. In one case the stronger fan is intake, which accelerates the flow out the others, or in the other it's exhaust, which accelerates flow in through the other intakes. They all work together as a system, but if you had your two strongest as the rear exhaust and as a side panel exhaust, you greatly decrease the flow through the power supply. "IF" your PSU has a good linearly ramping fan speed controller, it would just increase the PSU fan speed to compensate, but we can't assume it responds this well as many don't.
The shorter answer - put all the fans in any way you want then check all temps including the HDD, motherboard & video card, capacitors. Swap the fans around if you feel it is then of benefit to take some of the airflow from something plenty cool enough, and divert to another area not so cool.