Yes and no - well, maybe. I agree with having your case ventilation fans controlled automatically by your mobo. The problem is how easy that will be. The issue is the natch (or lack thereof) of fan type to mobo header control method.
Most cases that come with fans these days supply 3-pin fans because they are marginally cheaper. But the only way to control the speed of that fan design is to vary the voltage supplied to them (via Pin #2 from 12 VDC (full speed( down to about 5 VDC (nearly stalled). SOME mobos can do that. Some can not, and can only use the newer system, PWM Mode, which works for 4-speed fans only. It can be tricky to figure out which way your mobo can do things. If your mobo has the right capability, it works just fine. If not, you have a few choices.
Post back here exactly what make and model of mobo you are getting, and we can look up its specs and try to advise. Tell us the maker and model of your case so we can check the specs for its fans.