Fans and Z87-GD65 new build question

Hi.  I am waiting on all my parts for a new build this week.  I've only done one build before and that was over 4 years ago (i5-750 / MSI P55-GD65).  My question is regarding fans and how to control them on the Z87-GD65 mobo.  My case comes with three 140 mm 3-pin fans and a 3 fan 3-speed manual fan controller.  I've never used a fan controller before and would prefer to use SpeedFan or the BIOS to adjust speed fans based on CPU/GPU temperatures.  Will I be able to set up automatic speed control in BIOS or SpeedFan for all 3 fans with this motherboard?  Or do I need PWM fans to do so?  What if I want to install 2 extra fans?  Any help would be appreciated!
CPU: Intel Core i5-4670K 3.4GHz Quad-Core Processor
CPU Cooler: Phanteks PH-TC12DX_RD 68.5 CFM CPU Cooler 
Motherboard: MSI Z87-GD65 Gaming ATX LGA1150 Motherboard 
Memory: G.Skill Sniper Series 8GB (2 x 4GB) DDR3-1866 Memory 
Storage: Samsung 840 EVO 250GB 2.5" Solid State Disk
Video Card: Sapphire Radeon HD 7950 3GB Video Card
Case: Fractal Design Arc Midi R2 (Black) ATX Mid Tower Case
Power Supply: SeaSonic G 550W 80+ Gold Certified Semi-Modular ATX Power Supply

Those connected to the fan controllers are controlled through their buttons (or whatever to adjust the speed). Those connected to motherboard, are connected through a software, such as Command Centre (which in my opinion is great for this).
Not sure how many connectors do you have on the motherboard, but I think there's x2 CPUFan and x3 SysFan. That means you can have x5 fans connected to them. But you can either purchase a Y splitter which will let you connect 2 fans into a single socket (I am using one Y splitter) or just get proper fan controller.

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