New build. Using SSD for primary drive then will also install (2) mechanical data drives in raid.
The Z87-plus has (6) Sata 6g ports and can be configured to Raid. It also has (2) Sata 6G AS Media serial ports. Would I assume that the SSD should be connected to the AS Media Sata and the Intel ports used for the raid array? The AS Media Sata can only be set to AHCI mode. These ports are indicated to be for data only.
Stick with the Intel 6G ports. You should always avoid using 3rd party controllers when given a choice. I would also skip the RAID unless you're doing it for redundancy. It's generally not worth the headache, especially if it's a mechanical drive that's going to be used mainly for media storage.