I was wondering what your approach is to using available SATA ports for your array.
I have six MB SATA ports and eight SATA available via HBA (9211-8i)
Do you recommend populating all available motherboard SATA ports first, then using an HBA for the rest of the array? Is it better to have all of the data disks if possible on the HBA first as a priority?
Do you guys recommend keeping many disks as possible on the same controller? (i.e. populating HBA first)
Yep; unless you need SAS support I would recommend onboard SATA first.
OP, I have the same HBA card as you, it gets toasty even just idling, and even hotter once you throw a load onto it. I measured ~10W power use just idling (no drives attached to HBA). I almost guarantee using onboard SATA will be more power efficient.
Even better, is if you can physically remove the HBA card until you need it.