It depends on the amount of fans you plan to connect to your MoBo.
If your MoBo has 1-2 4-pin fan headers and you plan to connect 2-4 fans to it, then use Y-splitter by connecting 2 fans to one MoBo fan header. But if you have 6+ fans, use PWM fan hub.
It's simple how the PWM fan hub works.
1. It has separate power connection from PSU (molex or SATA).
2. It has PWM wire that goes from PWM fan hub to any MoBo 4-pin SYS_FAN header.
3. Connect fans directly to the PWM fan hub.
You can only read the RPM of 1st slot fan while the PWM signal is divided between all connected fans and all fans run in sync.
For controlling each fan separately, you need a fan controller, e.g:
internal - NZXT GRID+ v2, specs:
https://www.nzxt.com/products/grid-plus-v2
external - NZXT Sentry 3, specs:
https://www.nzxt.com/products/sentry-3
(Note: external fan controllers mount to the 5.25" bay and there's far wider selection of them than internal fan controllers.)
In my Skylake build (full specs in my sig), i have 7 case fans and external fan controller to give me absolute control over the 6 fans connected to there. Few pics too,
link: http://www.tomshardware.co.uk/forum/id-3272328/show-newest-system-upgrade-components/page-5.html#19565270