What's the best way to connect 8 or 12 hdds? The only board I've found on Newegg with 8 sata ports has 6 Intel ports and 2 ASmedia ports, plus it's expensive. I've always read Intel ports are preferably for your (primary?) hdd over third party ones. Would it be alright to use the ASmedia ports in this case?
Would it be better, or at least an option, to add a 2x sata pci-e card to the motherboard for more drives?
You get the same Read/Write performance if you connect the HDDs to the Intel or the 3rd party (ASMedia, Marvell) SATA ports.
No HDD can spin fast enough to saturate a SATA 2 (3Gb/s) port, let alone a SATA 3 (6Gb/s) port.
It's when you are connecting SSDs when it makes a difference. The 3rd party controllers were developed when 1st generation SSDs were made. They can't handle the speeds of current generation SSDs. If you connect a current generation SSD to a 3rd party port it will get SATA 3 speeds, but it won't get maximum advertised SATA 3 speeds.
If you need to connect more than 8 HDDs then yes, add a PCIe card (minimum x2) for additional ports.