Yes, that mobo detail does make a difference. Its manual on p. 3-39 shows clearly that it has four 4-pin CHA_FAN headers each separately configurable with several options. These are the places to connect your case ventilation fans. One option important for you is that each header can be set to operate either in PWM Mode for 4-pin fans, or in DC Mode for 3-pin fans. So your situation becomes easy: you connect that pre-installed rear 3-pin fan to one of the CHA_FAN headers and set that header in BIOS Setup under the heading "Chassis Fan 1-4 Q-Fan Control" to DC Mode. You can do the same thing if you choose additional 3-pin fans, even if you combine two or three 3-pin fans with a splitter to one CHA_FAN header. If you buy any 4-pin fans to add, you would connect those to a different CHA_FAN header and set it to use the PWM Mode.
It's getting hard to find 3-pin fan splitters these days, but that's no problem. You can use a 4-pin fan splitter and plug into its output arms either 3- or 4-pin fans. Here are some with 2 or 3 outputs from one mobo 4-pin fan header.
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423160&cm_re=fan_splitter-_-12-423-160-_-Product
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423162&cm_re=fan_splitter-_-12-423-162-_-Product
Note one correct design element of these: among the output connectors, only one has all its four pins. The others are missing Pin #3 to ensure that the mobo receives only the speed signal from ONE of the fans connected to the splitter.
Other notes on configuring your mobo fan headers.
1. Manual p. 3-39, "Chassis Fan 1-4 Q-Fan Source" should be set to MotherBoard (NOT to CPU) so the case fans will be guided by the temperature sensor built into the mobo, and not the sensor inside the CPU chip.
2. p. 3-40, "Chassis Fan 1-4 Profile" should be Standard (the default setting) to allow automatic control of your fans by the mobo.
Now to choice of fans. I have a preference for Noctua units because they are pretty quiet, blow a lot of air, and are very reliable with a 6-year warranty (and users report they do last a long time). However, others are less enthusiastic, and it is true that Noctua fans sometimes are more expensive.
For your case I would suggest a total of four fans: the 140 mm 3-pin unit already included with your case, plus three more 140 mm units. They should be arranged as two in the front as air intakes, and the pre-installed rear one as exhaust, plus one mounted in the top as exhaust. This will balance air intake and exhaust. Personally I prefer to have slightly more intake than exhaust, so I might suggest changing the top exhaust to a smaller 120 mm unit, but that's up to you. Don't forget as time goes on to remove and clean the air intake dust filters in the case front and also on the bottom for the PSU's air intake.
For Noctua's 140 mm line they say you don't need to be concerned about low or high pressure questions because they are all OK. (Some fan makers recommend low-pressure fans for uninhibited fans like case ventilation, and high-pressure ones for CPU coolers with narrow air channels that restrict air flow.) So with those thoughts, you could consider from Noctua their model NF-A14 PWM, a 4-pin unit that delivers max 82 cu ft/min air flow with max noise just under 25 dBA. That model comes only in a 2-tone brown and sells for about US$21. A different model NF-P14s redux-1500 PWM delivers slightly less air at 79 cu ft/min and one dBA higher noise (not really different) comes in 2-tone grey which might hide better behind the black front intake grilles; cheaper at about US$16. There are similar 120 mm models. Noctua also has its industrialPPC line that cost more, run faster and use more electrical power, and deliver much more air at higher noise levels. You probably don't need those, but FYI.
For a comparison point, the 3-pin Phanteks PH-F140 SP 3-pin fan included with your case delivers max 83 CFM air flow at 19 dBA noise, has a 5-year warranty, sells for US$15.
Some others to consider.
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423162&cm_re=fan_splitter-_-12-423-162-_-Product
a 3-pin fan, max 55 CFM with 22 dBA noise, 1 year warranty, US$9
http://www.newegg.com/Product/Product.aspx?Item=N82E16835181028&cm_re=fan_140mm-_-35-181-028-_-Product
a 3-pin fan max 68 CFM, 24 dBA noise, 2 year warranty, US$18
http://www.newegg.com/Product/Product.aspx?Item=N82E16835553007&cm_re=fan_140mm-_-35-553-007-_-Product
a 3-pin fan, max 70 CFM, 19 dBA, 1 year warranty, US$18
http://www.newegg.com/Product/Product.aspx?Item=N82E16835200067&cm_re=fan_140mm-_-35-200-067-_-Product
a 4-pin fan, 90 CFM, 22 dBA, 1 year warranty, US$13
http://www.newegg.com/Product/Product.aspx?Item=N82E16835553016&cm_re=fan_140mm-_-35-553-016-_-Product
a 4-pin fan with orange blades, 70 CFM, 19 dBA, 1 year warranty, US$19
You certainly can look around for other fans and other sources to get the best prices. I suggest you concentrate on the air flow rating first, the noise level second, then price and warranty.
There are lots of fans sold as "low noise" models, and others that come with "low noise adapters". Both of these types depend on running the fan slower for less noise, AND less air flow. I recommend you do not bother with those. You will have your mobo control all your case fans, which means that automatically they will run as slow as they can and still deliver the air flow required to cool your case properly. Of course, that means they will normally be much quieter than their max noise levels. The Low Noise designs are best suited to people who do not use automatic fan speed control and connect them to a fixed 12 VDC power supply so the fans are running full speed all the time making more noise (and air flow) than needed.
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