The Pro M is a budget case and, as I recall, to meet this price target, I don't think it comes with the Phanteks Fan Hub. It makes the number of fan headers you have MoBo immaterial.
The Phanteks cases fortunately come with the best 140mm fans on the market. Therefere the best thing you can do with fans, is "more of the same"
http://www.silentpcreview.com/article1345-page7.html
Be aware tho, following "conventional logic" will not serve you will if you are going to fill all 5 fan mounts.
Top = 2 x 140mm
Front = 2 x 140mm
Rear = 1 x 140mm (pre-installed)
Of course determining your needs is impossible w/o knowing what is going on the case. Let's assume a GTX 1080 + OC'd CPU
130 watts OC'd CPU + 220 watts OC'd GPU = 350 watts....
Figure on 75 to 100 watts per fan if quiet is important ... stretch that a bit if you don't mind them running at full speed. 3 fans would give you about 117 watts per fan. Put them in the front as intakes. If you have more load or want more quiet, then I'd go with 5 fans ... and I am sure your 1st inclination would be to install them on top a exhausts.
Here's why that's a bad idea .... You'd have 3 out and 2 in... with the in restricted by inlet filters created negative pressure. If you use a fog machine to test as we have with the Enthoo Pro, the PSU and the GFX card are exhausting hot air out the back ... which gets sucked right back in thru the rear case grille because of the negative pressure. Reversing the top fans, we have 4 in and 1 out, forcing all air out the rear of the case and no hot air or dust being sucked back in.
Choices:
1. Connect your fans to three Chassis (CHA) or System (SYS) headers. Of not autoselect, make sure that if its a newer MoBo, they are set to DCV control. Most new MoBs are autoselect and provide PWM or DCV
2. Purchase the Phanteks Fan Hub $20; connect the Hub to a PWM header ... and then connect the DCV fans to the Hub... the hub provides a best of both works situation, converting the PWM signal to DCV giving you all the advantages of PWM (low speed control) and none of the disadvantages (cost, low speed hum / clicking).
3. You can control the fans thru MoBo utility or BIOS.
You can also use fan splitters if you don't have enough headers ($2.99 on Phanteks site) but the cabling gets messy. Make sure not to put more than 1 amp worth of fans on any one header. The Phanteks fans are rated at 0.14 amps each.
Having done builds in almost all Phanteks cases, we find that they operate well set up as follows (assuming your MoBo Software has these capabilities)
CPU Cooler Fans (325 - 1250 rpm)
Case Fans (375 - 850 rpm, shut off below 375 rpm)
Fan Hub
http://www.newegg.com/Product/Product.aspx?Item=N82E16811984004
Fans (Just missed a newegg sale.... been $12 to $15 last few weeks.
http://www.newegg.com/Product/Product.aspx?Item=N82E16835709022