It's not best, it's a different way. To connect to the Mobo you need the mini 3 pin connectors. Some fans have them, some don't. If you connect them to the mobo, then you can control the speeds by the bios and the temps your Mobo reports.
Most of us use the Mobo headers to control fans that blow directly onto Mobo parts. Like The CPU cooler, a fan for the NB, one for the mem etc.
Case fans are for general air flow and really don't need to be adjusted. I had a 900, put the two front on low, back one on med, get one for the door, put on Low, and the top 200mm on Med. Silent and great airflow in the case.
If you must have adjustable fans on the case, get a fan controller to control them all.